From 29ea2f08b01624c2b5d0832fe82e989cfb823a1c Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Sun, 20 Oct 2024 16:26:04 +0000
Subject: [PATCH] Update pkgdown documentation
 bd6fa4b039bd5e4ce914ff71740bb478f181c004

---
 main/404.html                                 | 33 +---------------
 main/CODE_OF_CONDUCT.html                     | 33 +---------------
 main/CONTRIBUTING.html                        | 33 +---------------
 main/LICENSE-text.html                        | 33 +---------------
 main/SECURITY.html                            | 33 +---------------
 main/articles/index.html                      | 33 +---------------
 main/articles/missing_values.html             | 33 +---------------
 main/articles/tables.html                     | 33 +---------------
 main/articles/tern.html                       | 33 +---------------
 main/articles/tern_formats.html               | 33 +---------------
 main/authors.html                             | 37 ++----------------
 main/index.html                               | 33 +---------------
 main/news/index.html                          | 37 ++----------------
 main/pkgdown.yml                              |  2 +-
 main/reference/abnormal.html                  | 37 ++----------------
 main/reference/abnormal_by_baseline.html      | 37 ++----------------
 main/reference/abnormal_by_marked.html        | 37 ++----------------
 main/reference/abnormal_by_worst_grade.html   | 37 ++----------------
 .../abnormal_by_worst_grade_worsen.html       | 37 ++----------------
 main/reference/add_riskdiff.html              | 33 +---------------
 main/reference/add_rowcounts.html             | 33 +---------------
 main/reference/aesi_label.html                | 33 +---------------
 main/reference/afun_riskdiff.html             | 33 +---------------
 main/reference/afun_selected_stats.html       | 33 +---------------
 main/reference/analyze_colvars_functions.html | 33 +---------------
 main/reference/analyze_functions.html         | 33 +---------------
 main/reference/analyze_variables.html         | 39 ++-----------------
 main/reference/analyze_vars_in_cols.html      | 33 +---------------
 main/reference/append_varlabels.html          | 33 +---------------
 main/reference/apply_auto_formatting.html     | 33 +---------------
 main/reference/argument_convention.html       | 33 +---------------
 main/reference/arrange_grobs.html             | 33 +---------------
 main/reference/as.rtable.html                 | 33 +---------------
 main/reference/as_factor_keep_attributes.html | 33 +---------------
 main/reference/assertions.html                | 33 +---------------
 main/reference/bins_percent_labels.html       | 33 +---------------
 main/reference/c_label_n.html                 | 33 +---------------
 main/reference/c_label_n_alt.html             | 33 +---------------
 main/reference/cfun_by_flag.html              | 33 +---------------
 main/reference/check_diff_prop_ci.html        | 33 +---------------
 main/reference/check_same_n.html              | 33 +---------------
 main/reference/combination_function.html      | 33 +---------------
 main/reference/combine_counts.html            | 33 +---------------
 main/reference/combine_groups.html            | 33 +---------------
 main/reference/combine_levels.html            | 33 +---------------
 main/reference/combine_vectors.html           | 33 +---------------
 main/reference/compare_variables.html         | 39 ++-----------------
 main/reference/control_analyze_vars.html      | 33 +---------------
 main/reference/control_annot.html             | 33 +---------------
 main/reference/control_coxph.html             | 33 +---------------
 main/reference/control_coxreg.html            | 33 +---------------
 main/reference/control_incidence_rate.html    | 33 +---------------
 main/reference/control_lineplot_vars.html     | 33 +---------------
 main/reference/control_logistic.html          | 33 +---------------
 main/reference/control_riskdiff.html          | 33 +---------------
 main/reference/control_step.html              | 33 +---------------
 main/reference/control_surv_time.html         | 33 +---------------
 main/reference/control_surv_timepoint.html    | 33 +---------------
 main/reference/count_cumulative.html          | 37 ++----------------
 main/reference/count_missed_doses.html        | 37 ++----------------
 main/reference/count_occurrences.html         | 37 ++----------------
 .../reference/count_occurrences_by_grade.html | 37 ++----------------
 .../count_patients_events_in_cols.html        | 39 ++-----------------
 main/reference/count_patients_with_event.html | 37 ++----------------
 main/reference/count_patients_with_flags.html | 37 ++----------------
 main/reference/count_values.html              | 37 ++----------------
 main/reference/cox_regression.html            | 33 +---------------
 main/reference/cox_regression_inter.html      | 33 +---------------
 main/reference/cut_quantile_bins.html         | 33 +---------------
 .../d_count_abnormal_by_baseline.html         | 33 +---------------
 main/reference/d_count_cumulative.html        | 33 +---------------
 main/reference/d_count_missed_doses.html      | 33 +---------------
 main/reference/d_onco_rsp_label.html          | 33 +---------------
 main/reference/d_pkparam.html                 | 33 +---------------
 main/reference/d_proportion.html              | 33 +---------------
 main/reference/d_proportion_diff.html         | 33 +---------------
 main/reference/d_rsp_subgroups_colvars.html   | 33 +---------------
 .../d_survival_subgroups_colvars.html         | 33 +---------------
 main/reference/d_test_proportion_diff.html    | 33 +---------------
 main/reference/day2month.html                 | 33 +---------------
 main/reference/decorate_grob.html             | 33 +---------------
 main/reference/decorate_grob_factory.html     | 33 +---------------
 main/reference/decorate_grob_set.html         | 33 +---------------
 main/reference/default_na_str.html            | 33 +---------------
 .../default_stats_formats_labels.html         | 33 +---------------
 main/reference/desctools_binom.html           | 33 +---------------
 main/reference/df2gg.html                     | 33 +---------------
 main/reference/df_explicit_na.html            | 33 +---------------
 main/reference/dot-is_equal_float.html        | 33 +---------------
 main/reference/draw_grob.html                 | 33 +---------------
 main/reference/empty_vector_if_na.html        | 33 +---------------
 main/reference/estimate_coef.html             | 33 +---------------
 main/reference/estimate_multinomial_rsp.html  | 37 ++----------------
 main/reference/estimate_proportion.html       | 37 ++----------------
 main/reference/ex_data.html                   | 33 +---------------
 main/reference/explicit_na.html               | 33 +---------------
 main/reference/extract_by_name.html           | 33 +---------------
 main/reference/extract_rsp_biomarkers.html    | 33 +---------------
 main/reference/extract_rsp_subgroups.html     | 33 +---------------
 .../extract_survival_biomarkers.html          | 33 +---------------
 .../reference/extract_survival_subgroups.html | 33 +---------------
 main/reference/extreme_format.html            | 33 +---------------
 main/reference/f_conf_level.html              | 33 +---------------
 main/reference/f_pval.html                    | 33 +---------------
 main/reference/fct_collapse_only.html         | 33 +---------------
 main/reference/fct_discard.html               | 33 +---------------
 main/reference/fct_explicit_na_if.html        | 33 +---------------
 main/reference/fit_coxreg.html                | 33 +---------------
 main/reference/fit_logistic.html              | 33 +---------------
 main/reference/fit_rsp_step.html              | 33 +---------------
 main/reference/fit_survival_step.html         | 33 +---------------
 main/reference/forest_viewport.html           | 33 +---------------
 main/reference/format_auto.html               | 33 +---------------
 main/reference/format_count_fraction.html     | 33 +---------------
 .../format_count_fraction_fixed_dp.html       | 33 +---------------
 .../reference/format_count_fraction_lt10.html | 33 +---------------
 main/reference/format_extreme_values.html     | 33 +---------------
 main/reference/format_extreme_values_ci.html  | 33 +---------------
 main/reference/format_fraction.html           | 33 +---------------
 main/reference/format_fraction_fixed_dp.html  | 33 +---------------
 main/reference/format_fraction_threshold.html | 33 +---------------
 main/reference/format_sigfig.html             | 33 +---------------
 main/reference/format_xx.html                 | 33 +---------------
 main/reference/formatting_functions.html      | 33 +---------------
 main/reference/g_bland_altman.html            | 33 +---------------
 main/reference/g_forest.html                  | 33 +---------------
 main/reference/g_ipp.html                     | 33 +---------------
 main/reference/g_km.html                      | 33 +---------------
 main/reference/g_lineplot.html                | 33 +---------------
 main/reference/g_step.html                    | 33 +---------------
 main/reference/g_waterfall.html               | 33 +---------------
 main/reference/get_covariates.html            | 33 +---------------
 main/reference/get_smooths.html               | 33 +---------------
 main/reference/groups_list_to_df.html         | 33 +---------------
 .../h_adlb_abnormal_by_worst_grade.html       | 33 +---------------
 main/reference/h_adlb_worsen.html             | 33 +---------------
 .../h_adsl_adlb_merge_using_worst_flag.html   | 33 +---------------
 main/reference/h_ancova.html                  | 33 +---------------
 main/reference/h_append_grade_groups.html     | 33 +---------------
 main/reference/h_col_indices.html             | 33 +---------------
 main/reference/h_count_cumulative.html        | 33 +---------------
 main/reference/h_cox_regression.html          | 33 +---------------
 main/reference/h_data_plot.html               | 33 +---------------
 main/reference/h_decompose_gg.html            | 33 +---------------
 main/reference/h_format_row.html              | 33 +---------------
 main/reference/h_g_ipp.html                   | 33 +---------------
 main/reference/h_ggkm.html                    | 33 +---------------
 main/reference/h_glm_count.html               | 33 +---------------
 main/reference/h_grob_coxph.html              | 33 +---------------
 main/reference/h_grob_median_surv.html        | 33 +---------------
 main/reference/h_grob_tbl_at_risk.html        | 33 +---------------
 main/reference/h_grob_y_annot.html            | 33 +---------------
 main/reference/h_incidence_rate.html          | 33 +---------------
 main/reference/h_km_layout.html               | 33 +---------------
 main/reference/h_logistic_regression.html     | 33 +---------------
 main/reference/h_map_for_count_abnormal.html  | 33 +---------------
 main/reference/h_odds_ratio.html              | 33 +---------------
 main/reference/h_pkparam_sort.html            | 33 +---------------
 main/reference/h_ppmeans.html                 | 33 +---------------
 main/reference/h_prop_diff.html               | 33 +---------------
 main/reference/h_prop_diff_test.html          | 33 +---------------
 main/reference/h_proportions.html             | 33 +---------------
 .../h_response_biomarkers_subgroups.html      | 33 +---------------
 main/reference/h_response_subgroups.html      | 33 +---------------
 main/reference/h_split_by_subgroups.html      | 33 +---------------
 main/reference/h_split_param.html             | 33 +---------------
 main/reference/h_stack_by_baskets.html        | 33 +---------------
 main/reference/h_step.html                    | 33 +---------------
 .../h_survival_biomarkers_subgroups.html      | 33 +---------------
 .../h_survival_duration_subgroups.html        | 33 +---------------
 main/reference/h_tab_one_biomarker.html       | 33 +---------------
 main/reference/h_tbl_coxph_pairwise.html      | 33 +---------------
 main/reference/h_tbl_median_surv.html         | 33 +---------------
 main/reference/h_worsen_counter.html          | 33 +---------------
 main/reference/h_xticks.html                  | 33 +---------------
 main/reference/imputation_rule.html           | 33 +---------------
 main/reference/incidence_rate.html            | 37 ++----------------
 main/reference/index.html                     | 33 +---------------
 main/reference/labels_or_names.html           | 33 +---------------
 main/reference/labels_use_control.html        | 33 +---------------
 main/reference/logistic_regression_cols.html  | 33 +---------------
 main/reference/logistic_summary_by_flag.html  | 33 +---------------
 main/reference/make_names.html                | 33 +---------------
 main/reference/month2day.html                 | 33 +---------------
 main/reference/muffled_car_anova.html         | 33 +---------------
 main/reference/n_available.html               | 33 +---------------
 main/reference/odds_ratio.html                | 37 ++----------------
 main/reference/prop_diff.html                 | 37 ++----------------
 main/reference/prop_diff_test.html            | 37 ++----------------
 main/reference/prune_occurrences.html         | 33 +---------------
 main/reference/range_noinf.html               | 33 +---------------
 main/reference/reapply_varlabels.html         | 33 +---------------
 .../response_biomarkers_subgroups.html        | 33 +---------------
 main/reference/response_subgroups.html        | 33 +---------------
 main/reference/rtable2gg.html                 | 33 +---------------
 main/reference/rtables_access.html            | 33 +---------------
 main/reference/s_bland_altman.html            | 33 +---------------
 main/reference/s_cox_multivariate.html        | 33 +---------------
 main/reference/sas_na.html                    | 33 +---------------
 main/reference/score_occurrences.html         | 33 +---------------
 main/reference/split_cols_by_groups.html      | 33 +---------------
 main/reference/split_text_grob.html           | 33 +---------------
 main/reference/stack_grobs.html               | 33 +---------------
 main/reference/stat_mean_ci.html              | 33 +---------------
 main/reference/stat_mean_pval.html            | 33 +---------------
 main/reference/stat_median_ci.html            | 33 +---------------
 main/reference/stat_propdiff_ci.html          | 33 +---------------
 main/reference/strata_normal_quantile.html    | 33 +---------------
 main/reference/study_arm.html                 | 33 +---------------
 main/reference/summarize_ancova.html          | 37 ++----------------
 main/reference/summarize_change.html          | 37 ++----------------
 main/reference/summarize_colvars.html         | 33 +---------------
 main/reference/summarize_functions.html       | 33 +---------------
 main/reference/summarize_glm_count.html       | 37 ++----------------
 main/reference/summarize_logistic.html        | 33 +---------------
 main/reference/summarize_num_patients.html    | 37 ++----------------
 .../summarize_patients_exposure_in_cols.html  | 37 ++----------------
 .../survival_biomarkers_subgroups.html        | 33 +---------------
 main/reference/survival_coxph_pairwise.html   | 37 ++----------------
 .../survival_duration_subgroups.html          | 33 +---------------
 main/reference/survival_time.html             | 37 ++----------------
 main/reference/survival_timepoint.html        | 37 ++----------------
 main/reference/tern-package.html              | 33 +---------------
 main/reference/tidy.glm.html                  | 33 +---------------
 main/reference/tidy.step.html                 | 33 +---------------
 main/reference/tidy_coxreg.html               | 33 +---------------
 main/reference/to_n.html                      | 33 +---------------
 main/reference/to_string_matrix.html          | 33 +---------------
 main/reference/try_car_anova.html             | 33 +---------------
 main/reference/ungroup_stats.html             | 33 +---------------
 main/reference/univariate.html                | 33 +---------------
 main/reference/unlist_and_blank_na.html       | 33 +---------------
 .../update_weights_strat_wilson.html          | 33 +---------------
 main/reference/utils_split_funs.html          | 33 +---------------
 main/search.json                              |  2 +-
 235 files changed, 300 insertions(+), 7523 deletions(-)

diff --git a/main/404.html b/main/404.html
index dacf60abf9..b6d189c5bb 100644
--- a/main/404.html
+++ b/main/404.html
@@ -29,7 +29,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,37 +50,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="https://insightsengineering.github.io/tern/news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html
index 3f36d165d9..bf3e15783b 100644
--- a/main/CODE_OF_CONDUCT.html
+++ b/main/CODE_OF_CONDUCT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index f066c058a8..5964bd88dd 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html
index 6fce8b80c5..54a0e876d4 100644
--- a/main/LICENSE-text.html
+++ b/main/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/SECURITY.html b/main/SECURITY.html
index 1f9118e2bb..e06b0f80b2 100644
--- a/main/SECURITY.html
+++ b/main/SECURITY.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
diff --git a/main/articles/index.html b/main/articles/index.html
index 17a06a1404..4555249684 100644
--- a/main/articles/index.html
+++ b/main/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/articles/missing_values.html b/main/articles/missing_values.html
index 2ddfe123c5..04fc413b1b 100644
--- a/main/articles/missing_values.html
+++ b/main/articles/missing_values.html
@@ -28,7 +28,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,37 +49,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/articles/tables.html b/main/articles/tables.html
index 73e7cc8429..588c9c1949 100644
--- a/main/articles/tables.html
+++ b/main/articles/tables.html
@@ -28,7 +28,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,37 +49,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/articles/tern.html b/main/articles/tern.html
index 2f17405541..de98c2c5ee 100644
--- a/main/articles/tern.html
+++ b/main/articles/tern.html
@@ -28,7 +28,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,37 +49,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/articles/tern_formats.html b/main/articles/tern_formats.html
index 2d156cb417..338df58275 100644
--- a/main/articles/tern_formats.html
+++ b/main/articles/tern_formats.html
@@ -28,7 +28,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,37 +49,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
diff --git a/main/authors.html b/main/authors.html
index d5c07bd088..dc81165490 100644
--- a/main/authors.html
+++ b/main/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="unit-test-report/">Unit test report</a></li>
@@ -137,14 +106,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Zhu J, Sabanés Bové D, Stoilova J, Garolini D, de la Rua E, Yogasekaram A, Wang H, Collin F, Waddell A, Rucki P, Liao C, Li J (2024).
 <em>tern: Create Common TLGs Used in Clinical Trials</em>.
-R package version 0.9.6.9005,
+R package version 0.9.6.9006,
 https://github.com/insightsengineering/tern/, <a href="https://insightsengineering.github.io/tern/">https://insightsengineering.github.io/tern/</a>.
 </p>
       <pre>@Manual{,
   title = {tern: Create Common TLGs Used in Clinical Trials},
   author = {Joe Zhu and Daniel {Sabanés Bové} and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Heng Wang and Francois Collin and Adrian Waddell and Pawel Rucki and Chendi Liao and Jennifer Li},
   year = {2024},
-  note = {R package version 0.9.6.9005,
+  note = {R package version 0.9.6.9006,
     https://github.com/insightsengineering/tern/},
   url = {https://insightsengineering.github.io/tern/},
 }</pre>
diff --git a/main/index.html b/main/index.html
index 376a05c073..96535a5e77 100644
--- a/main/index.html
+++ b/main/index.html
@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -52,37 +52,6 @@
 </li>
 <li class="nav-item"><a class="nav-link" href="news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports">
 <li><a class="dropdown-item" href="coverage-report/">Coverage report</a></li>
diff --git a/main/news/index.html b/main/news/index.html
index b8ce2839c9..b1be612890 100644
--- a/main/news/index.html
+++ b/main/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="active nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -76,9 +45,9 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.9.6.9005" id="tern-0969005">tern 0.9.6.9005<a class="anchor" aria-label="anchor" href="#tern-0969005"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.9.6.9006" id="tern-0969006">tern 0.9.6.9006<a class="anchor" aria-label="anchor" href="#tern-0969006"></a></h2>
 <div class="section level4">
-<h4 id="bug-fixes-0-9-6-9005">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6-9005"></a></h4>
+<h4 id="bug-fixes-0-9-6-9006">Bug Fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-6-9006"></a></h4>
 <ul><li>Fixed bug in <code><a href="../reference/analyze_variables.html">a_summary()</a></code> causing non-unique <code>row_name</code> values to occur when multiple statistics are selected for count variables.</li>
 </ul></div>
 </div>
diff --git a/main/pkgdown.yml b/main/pkgdown.yml
index a805bc737f..cde2087c37 100644
--- a/main/pkgdown.yml
+++ b/main/pkgdown.yml
@@ -6,7 +6,7 @@ articles:
   tables: tables.html
   tern_formats: tern_formats.html
   tern: tern.html
-last_built: 2024-10-18T01:43Z
+last_built: 2024-10-20T16:23Z
 urls:
   reference: https://insightsengineering.github.io/tern/reference
   article: https://insightsengineering.github.io/tern/articles
diff --git a/main/reference/abnormal.html b/main/reference/abnormal.html
index 61566fa00a..1a27c47fb9 100644
--- a/main/reference/abnormal.html
+++ b/main/reference/abnormal.html
@@ -33,7 +33,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -51,37 +51,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -194,8 +163,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("abnormal")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/abnormal_by_baseline.html b/main/reference/abnormal_by_baseline.html
index 9c0a748368..ff79423986 100644
--- a/main/reference/abnormal_by_baseline.html
+++ b/main/reference/abnormal_by_baseline.html
@@ -59,7 +59,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -77,37 +77,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -223,8 +192,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("abnormal_by_baseline")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/abnormal_by_marked.html b/main/reference/abnormal_by_marked.html
index b776b58728..ae7c4b0bce 100644
--- a/main/reference/abnormal_by_marked.html
+++ b/main/reference/abnormal_by_marked.html
@@ -47,7 +47,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,37 +65,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -202,8 +171,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("abnormal_by_marked")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/abnormal_by_worst_grade.html b/main/reference/abnormal_by_worst_grade.html
index f1e297fbb9..0e9e6889a5 100644
--- a/main/reference/abnormal_by_worst_grade.html
+++ b/main/reference/abnormal_by_worst_grade.html
@@ -47,7 +47,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,37 +65,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -194,8 +163,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("abnormal_by_worst_grade")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/abnormal_by_worst_grade_worsen.html b/main/reference/abnormal_by_worst_grade_worsen.html
index 4759de1fbf..2894a1dfe8 100644
--- a/main/reference/abnormal_by_worst_grade_worsen.html
+++ b/main/reference/abnormal_by_worst_grade_worsen.html
@@ -43,7 +43,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -61,37 +61,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -195,8 +164,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("abnormal_by_worst_grade_worsen")</code>
-to see all available statistics.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'fraction'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/add_riskdiff.html b/main/reference/add_riskdiff.html
index 00d63c7a7a..8df1169be8 100644
--- a/main/reference/add_riskdiff.html
+++ b/main/reference/add_riskdiff.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/add_rowcounts.html b/main/reference/add_rowcounts.html
index b93f647ebd..cd7eb761a5 100644
--- a/main/reference/add_rowcounts.html
+++ b/main/reference/add_rowcounts.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/aesi_label.html b/main/reference/aesi_label.html
index 98d89f3fb4..895b3b9e92 100644
--- a/main/reference/aesi_label.html
+++ b/main/reference/aesi_label.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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diff --git a/main/reference/afun_riskdiff.html b/main/reference/afun_riskdiff.html
index 8c102857d3..9f54a3cf51 100644
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@@ -15,7 +15,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
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index c3d893ac6f..882d3b143d 100644
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@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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diff --git a/main/reference/analyze_colvars_functions.html b/main/reference/analyze_colvars_functions.html
index 55c6bea164..b0a7cf27be 100644
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+++ b/main/reference/analyze_colvars_functions.html
@@ -47,7 +47,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -65,37 +65,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/analyze_functions.html b/main/reference/analyze_functions.html
index e54227f25e..786866b8d6 100644
--- a/main/reference/analyze_functions.html
+++ b/main/reference/analyze_functions.html
@@ -75,7 +75,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -93,37 +93,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/analyze_variables.html b/main/reference/analyze_variables.html
index e828f64399..ab0a0cb650 100644
--- a/main/reference/analyze_variables.html
+++ b/main/reference/analyze_variables.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -228,9 +197,9 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("analyze_vars_numeric")</code> to see
-statistics available for numeric variables, and <code>get_stats("analyze_vars_counts")</code> for statistics available
-for non-numeric variables.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options for numeric variables are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv'</code></p>
+<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/analyze_vars_in_cols.html b/main/reference/analyze_vars_in_cols.html
index 1788d7f785..2fd14938a9 100644
--- a/main/reference/analyze_vars_in_cols.html
+++ b/main/reference/analyze_vars_in_cols.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/append_varlabels.html b/main/reference/append_varlabels.html
index e71afa97f8..e14465107c 100644
--- a/main/reference/append_varlabels.html
+++ b/main/reference/append_varlabels.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/apply_auto_formatting.html b/main/reference/apply_auto_formatting.html
index e00c48e877..d967e23852 100644
--- a/main/reference/apply_auto_formatting.html
+++ b/main/reference/apply_auto_formatting.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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diff --git a/main/reference/argument_convention.html b/main/reference/argument_convention.html
index f86848367a..5cebd3437e 100644
--- a/main/reference/argument_convention.html
+++ b/main/reference/argument_convention.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -27,37 +27,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
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diff --git a/main/reference/arrange_grobs.html b/main/reference/arrange_grobs.html
index 600211b48f..0eaef6726d 100644
--- a/main/reference/arrange_grobs.html
+++ b/main/reference/arrange_grobs.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/as.rtable.html b/main/reference/as.rtable.html
index bc9b941b14..0c26cb2835 100644
--- a/main/reference/as.rtable.html
+++ b/main/reference/as.rtable.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/as_factor_keep_attributes.html b/main/reference/as_factor_keep_attributes.html
index ddea1901d5..0313f2275d 100644
--- a/main/reference/as_factor_keep_attributes.html
+++ b/main/reference/as_factor_keep_attributes.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/assertions.html b/main/reference/assertions.html
index 03f93722c4..83d6b00d0a 100644
--- a/main/reference/assertions.html
+++ b/main/reference/assertions.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/bins_percent_labels.html b/main/reference/bins_percent_labels.html
index 10d98420a5..8988826376 100644
--- a/main/reference/bins_percent_labels.html
+++ b/main/reference/bins_percent_labels.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/c_label_n.html b/main/reference/c_label_n.html
index 91024f69e2..b4e46ca7b4 100644
--- a/main/reference/c_label_n.html
+++ b/main/reference/c_label_n.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/c_label_n_alt.html b/main/reference/c_label_n_alt.html
index c01553904e..435e0f7b11 100644
--- a/main/reference/c_label_n_alt.html
+++ b/main/reference/c_label_n_alt.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/cfun_by_flag.html b/main/reference/cfun_by_flag.html
index 7a5ca88d90..f106a439c2 100644
--- a/main/reference/cfun_by_flag.html
+++ b/main/reference/cfun_by_flag.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/check_diff_prop_ci.html b/main/reference/check_diff_prop_ci.html
index f15a72818e..278b3199d4 100644
--- a/main/reference/check_diff_prop_ci.html
+++ b/main/reference/check_diff_prop_ci.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/check_same_n.html b/main/reference/check_same_n.html
index bd94e8f58d..fb8ec4eee2 100644
--- a/main/reference/check_same_n.html
+++ b/main/reference/check_same_n.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/combination_function.html b/main/reference/combination_function.html
index b3b06e9c5c..53b8adc0f1 100644
--- a/main/reference/combination_function.html
+++ b/main/reference/combination_function.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/combine_counts.html b/main/reference/combine_counts.html
index 2d36a7ebeb..581124feac 100644
--- a/main/reference/combine_counts.html
+++ b/main/reference/combine_counts.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/combine_groups.html b/main/reference/combine_groups.html
index babecee2ca..6584af5c31 100644
--- a/main/reference/combine_groups.html
+++ b/main/reference/combine_groups.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/combine_levels.html b/main/reference/combine_levels.html
index e2a4b48cdd..1f05b31665 100644
--- a/main/reference/combine_levels.html
+++ b/main/reference/combine_levels.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/combine_vectors.html b/main/reference/combine_vectors.html
index e518ed4faa..f32eba96de 100644
--- a/main/reference/combine_vectors.html
+++ b/main/reference/combine_vectors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/compare_variables.html b/main/reference/compare_variables.html
index 7b0f373220..b5d6e46b35 100644
--- a/main/reference/compare_variables.html
+++ b/main/reference/compare_variables.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -43,37 +43,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -199,9 +168,9 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run
-<code>get_stats("analyze_vars_numeric", add_pval = TRUE)</code> to see statistics available for numeric variables, and
-<code>get_stats("analyze_vars_counts", add_pval = TRUE)</code> for statistics available for non-numeric variables.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options for numeric variables are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'pval'</code></p>
+<p>Options for non-numeric variables are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/control_analyze_vars.html b/main/reference/control_analyze_vars.html
index 49fdaa45a3..855010798b 100644
--- a/main/reference/control_analyze_vars.html
+++ b/main/reference/control_analyze_vars.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/control_annot.html b/main/reference/control_annot.html
index 3c86c86cbb..c0a609583b 100644
--- a/main/reference/control_annot.html
+++ b/main/reference/control_annot.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/control_coxph.html b/main/reference/control_coxph.html
index bcfaa20274..6ee19980cc 100644
--- a/main/reference/control_coxph.html
+++ b/main/reference/control_coxph.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
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@@ -29,37 +29,6 @@
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diff --git a/main/reference/control_coxreg.html b/main/reference/control_coxreg.html
index 27cc6cc905..eafc682f88 100644
--- a/main/reference/control_coxreg.html
+++ b/main/reference/control_coxreg.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -27,37 +27,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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diff --git a/main/reference/control_incidence_rate.html b/main/reference/control_incidence_rate.html
index 072e76b422..f168c8db42 100644
--- a/main/reference/control_incidence_rate.html
+++ b/main/reference/control_incidence_rate.html
@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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diff --git a/main/reference/control_lineplot_vars.html b/main/reference/control_lineplot_vars.html
index bd4bc39387..137da84835 100644
--- a/main/reference/control_lineplot_vars.html
+++ b/main/reference/control_lineplot_vars.html
@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/control_logistic.html b/main/reference/control_logistic.html
index 9c14043de8..a31a40b9c8 100644
--- a/main/reference/control_logistic.html
+++ b/main/reference/control_logistic.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/control_riskdiff.html b/main/reference/control_riskdiff.html
index c8fe9e3c73..bb24124c4a 100644
--- a/main/reference/control_riskdiff.html
+++ b/main/reference/control_riskdiff.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/control_step.html b/main/reference/control_step.html
index e205912b0a..ba33409bd0 100644
--- a/main/reference/control_step.html
+++ b/main/reference/control_step.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/control_surv_time.html b/main/reference/control_surv_time.html
index 2611eef8f5..3d8e75417c 100644
--- a/main/reference/control_surv_time.html
+++ b/main/reference/control_surv_time.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/control_surv_timepoint.html b/main/reference/control_surv_timepoint.html
index a2b8768166..97b550cdb5 100644
--- a/main/reference/control_surv_timepoint.html
+++ b/main/reference/control_surv_timepoint.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/count_cumulative.html b/main/reference/count_cumulative.html
index 172dca1af2..c31519804f 100644
--- a/main/reference/count_cumulative.html
+++ b/main/reference/count_cumulative.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -39,37 +39,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -193,8 +162,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_cumulative")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_missed_doses.html b/main/reference/count_missed_doses.html
index 1f0c2e12fa..6e36a82ded 100644
--- a/main/reference/count_missed_doses.html
+++ b/main/reference/count_missed_doses.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -164,8 +133,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_missed_doses")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_occurrences.html b/main/reference/count_occurrences.html
index 875f672dcd..e3b879407a 100644
--- a/main/reference/count_occurrences.html
+++ b/main/reference/count_occurrences.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -41,37 +41,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -220,8 +189,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_occurrences")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_occurrences_by_grade.html b/main/reference/count_occurrences_by_grade.html
index 848125fad5..66756508b7 100644
--- a/main/reference/count_occurrences_by_grade.html
+++ b/main/reference/count_occurrences_by_grade.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,37 +45,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -232,8 +201,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_occurrences_by_grade")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'count_fraction', 'count_fraction_fixed_dp'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_patients_events_in_cols.html b/main/reference/count_patients_events_in_cols.html
index 5222bb44e4..d7d208ca86 100644
--- a/main/reference/count_patients_events_in_cols.html
+++ b/main/reference/count_patients_events_in_cols.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -155,9 +124,9 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run
-<code>get_stats("summarize_patients_events_in_cols")</code> to see available statistics for this function, in addition
-to any added using <code>filters_list</code>.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>In addition to any statistics added using <code>filters_list</code>, statistic options are:
+<code>'unique', 'all'</code></p></dd>
 
 
 <dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
diff --git a/main/reference/count_patients_with_event.html b/main/reference/count_patients_with_event.html
index 1145759371..604222054d 100644
--- a/main/reference/count_patients_with_event.html
+++ b/main/reference/count_patients_with_event.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -180,8 +149,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_patients_with_event")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_patients_with_flags.html b/main/reference/count_patients_with_flags.html
index 6fc2bd7219..af1b284263 100644
--- a/main/reference/count_patients_with_flags.html
+++ b/main/reference/count_patients_with_flags.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -194,8 +163,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_patients_with_flags")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/count_values.html b/main/reference/count_values.html
index b1b025b85e..58737fec32 100644
--- a/main/reference/count_values.html
+++ b/main/reference/count_values.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -175,8 +144,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("count_values")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/cox_regression.html b/main/reference/cox_regression.html
index ec3e3d218b..cbe31214d1 100644
--- a/main/reference/cox_regression.html
+++ b/main/reference/cox_regression.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/cox_regression_inter.html b/main/reference/cox_regression_inter.html
index 12d568f22c..4e93f9c6ac 100644
--- a/main/reference/cox_regression_inter.html
+++ b/main/reference/cox_regression_inter.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/cut_quantile_bins.html b/main/reference/cut_quantile_bins.html
index 3bc68f0f58..d6c97a1660 100644
--- a/main/reference/cut_quantile_bins.html
+++ b/main/reference/cut_quantile_bins.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_count_abnormal_by_baseline.html b/main/reference/d_count_abnormal_by_baseline.html
index d6723baaf7..3d9551cb0c 100644
--- a/main/reference/d_count_abnormal_by_baseline.html
+++ b/main/reference/d_count_abnormal_by_baseline.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_count_cumulative.html b/main/reference/d_count_cumulative.html
index 70eee9f8b6..13ccbfa352 100644
--- a/main/reference/d_count_cumulative.html
+++ b/main/reference/d_count_cumulative.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/d_count_missed_doses.html b/main/reference/d_count_missed_doses.html
index e69635b7cd..50fffb894a 100644
--- a/main/reference/d_count_missed_doses.html
+++ b/main/reference/d_count_missed_doses.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/d_onco_rsp_label.html b/main/reference/d_onco_rsp_label.html
index f9b2a885bc..e38604472f 100644
--- a/main/reference/d_onco_rsp_label.html
+++ b/main/reference/d_onco_rsp_label.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_pkparam.html b/main/reference/d_pkparam.html
index 1d2e17961b..c8a464aafa 100644
--- a/main/reference/d_pkparam.html
+++ b/main/reference/d_pkparam.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_proportion.html b/main/reference/d_proportion.html
index 5a3933ae8d..aba624ba75 100644
--- a/main/reference/d_proportion.html
+++ b/main/reference/d_proportion.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/d_proportion_diff.html b/main/reference/d_proportion_diff.html
index caf1d7090d..3b4d8e8f2a 100644
--- a/main/reference/d_proportion_diff.html
+++ b/main/reference/d_proportion_diff.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/d_rsp_subgroups_colvars.html b/main/reference/d_rsp_subgroups_colvars.html
index 066b998ffc..21b0d19e78 100644
--- a/main/reference/d_rsp_subgroups_colvars.html
+++ b/main/reference/d_rsp_subgroups_colvars.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item dropdown">
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_survival_subgroups_colvars.html b/main/reference/d_survival_subgroups_colvars.html
index 0764c4074a..af7a41017f 100644
--- a/main/reference/d_survival_subgroups_colvars.html
+++ b/main/reference/d_survival_subgroups_colvars.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/d_test_proportion_diff.html b/main/reference/d_test_proportion_diff.html
index ad1ea072ac..75c0305ad8 100644
--- a/main/reference/d_test_proportion_diff.html
+++ b/main/reference/d_test_proportion_diff.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/day2month.html b/main/reference/day2month.html
index 34af264e34..b39d0cb169 100644
--- a/main/reference/day2month.html
+++ b/main/reference/day2month.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/decorate_grob.html b/main/reference/decorate_grob.html
index d8960e4037..44d7aebcee 100644
--- a/main/reference/decorate_grob.html
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@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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diff --git a/main/reference/decorate_grob_factory.html b/main/reference/decorate_grob_factory.html
index e71f6e92bb..83a4c3d012 100644
--- a/main/reference/decorate_grob_factory.html
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@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/decorate_grob_set.html b/main/reference/decorate_grob_set.html
index fd08126123..e896ca83d3 100644
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@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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index 5a90dcad7e..854ecdb4a0 100644
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@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/default_stats_formats_labels.html b/main/reference/default_stats_formats_labels.html
index f784dbb9ca..b99fd95f1f 100644
--- a/main/reference/default_stats_formats_labels.html
+++ b/main/reference/default_stats_formats_labels.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/desctools_binom.html b/main/reference/desctools_binom.html
index 3cc00b41b7..1741fd49a5 100644
--- a/main/reference/desctools_binom.html
+++ b/main/reference/desctools_binom.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/df2gg.html b/main/reference/df2gg.html
index 6b018f9e46..0c5af522aa 100644
--- a/main/reference/df2gg.html
+++ b/main/reference/df2gg.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/df_explicit_na.html b/main/reference/df_explicit_na.html
index 1e87288663..9ef4a3e650 100644
--- a/main/reference/df_explicit_na.html
+++ b/main/reference/df_explicit_na.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/dot-is_equal_float.html b/main/reference/dot-is_equal_float.html
index 3c98cdd08a..edba6c4a22 100644
--- a/main/reference/dot-is_equal_float.html
+++ b/main/reference/dot-is_equal_float.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -25,37 +25,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/draw_grob.html b/main/reference/draw_grob.html
index 40d303d089..33081415f8 100644
--- a/main/reference/draw_grob.html
+++ b/main/reference/draw_grob.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -27,37 +27,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/empty_vector_if_na.html b/main/reference/empty_vector_if_na.html
index 27911875e9..d89b60f9cc 100644
--- a/main/reference/empty_vector_if_na.html
+++ b/main/reference/empty_vector_if_na.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/estimate_coef.html b/main/reference/estimate_coef.html
index 4993dae6b0..2c4b7a035f 100644
--- a/main/reference/estimate_coef.html
+++ b/main/reference/estimate_coef.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/estimate_multinomial_rsp.html b/main/reference/estimate_multinomial_rsp.html
index f4f1ef303f..d38e0c5a87 100644
--- a/main/reference/estimate_multinomial_rsp.html
+++ b/main/reference/estimate_multinomial_rsp.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -147,8 +116,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("estimate_multinomial_response")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_prop', 'prop_ci'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/estimate_proportion.html b/main/reference/estimate_proportion.html
index cf8024ae81..f62d1ea945 100644
--- a/main/reference/estimate_proportion.html
+++ b/main/reference/estimate_proportion.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -208,8 +177,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("estimate_proportion")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_prop', 'prop_ci'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/ex_data.html b/main/reference/ex_data.html
index 01a969d23f..a8315aeae3 100644
--- a/main/reference/ex_data.html
+++ b/main/reference/ex_data.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/explicit_na.html b/main/reference/explicit_na.html
index 4f6e452150..217d53a182 100644
--- a/main/reference/explicit_na.html
+++ b/main/reference/explicit_na.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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diff --git a/main/reference/extract_by_name.html b/main/reference/extract_by_name.html
index 369ec4cd9a..de8edd2f35 100644
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@@ -9,7 +9,7 @@
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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diff --git a/main/reference/extract_rsp_biomarkers.html b/main/reference/extract_rsp_biomarkers.html
index 5df380b0b6..1c8a598bb4 100644
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@@ -21,7 +21,7 @@
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
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diff --git a/main/reference/extract_rsp_subgroups.html b/main/reference/extract_rsp_subgroups.html
index dcfcb3d438..bcfb0e0b51 100644
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@@ -17,7 +17,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/extract_survival_biomarkers.html b/main/reference/extract_survival_biomarkers.html
index 1ff147ea0e..3fab8221c5 100644
--- a/main/reference/extract_survival_biomarkers.html
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@@ -17,7 +17,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -35,37 +35,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/extract_survival_subgroups.html b/main/reference/extract_survival_subgroups.html
index 576684c29a..ea4e1c621d 100644
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+++ b/main/reference/extract_survival_subgroups.html
@@ -17,7 +17,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -35,37 +35,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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diff --git a/main/reference/extreme_format.html b/main/reference/extreme_format.html
index 2f59e328a9..afbea524d3 100644
--- a/main/reference/extreme_format.html
+++ b/main/reference/extreme_format.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/f_conf_level.html b/main/reference/f_conf_level.html
index f5100cce86..19f39efc07 100644
--- a/main/reference/f_conf_level.html
+++ b/main/reference/f_conf_level.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/f_pval.html b/main/reference/f_pval.html
index afc89f591c..cf60c1df60 100644
--- a/main/reference/f_pval.html
+++ b/main/reference/f_pval.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fct_collapse_only.html b/main/reference/fct_collapse_only.html
index 214975a002..8ff7a59d1d 100644
--- a/main/reference/fct_collapse_only.html
+++ b/main/reference/fct_collapse_only.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fct_discard.html b/main/reference/fct_discard.html
index e92a09c1b7..78fd5caff9 100644
--- a/main/reference/fct_discard.html
+++ b/main/reference/fct_discard.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fct_explicit_na_if.html b/main/reference/fct_explicit_na_if.html
index 71079951e9..cd4bffc638 100644
--- a/main/reference/fct_explicit_na_if.html
+++ b/main/reference/fct_explicit_na_if.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fit_coxreg.html b/main/reference/fit_coxreg.html
index b075f538b3..214abf5338 100644
--- a/main/reference/fit_coxreg.html
+++ b/main/reference/fit_coxreg.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/fit_logistic.html b/main/reference/fit_logistic.html
index 86384794d5..a3d0c1771f 100644
--- a/main/reference/fit_logistic.html
+++ b/main/reference/fit_logistic.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fit_rsp_step.html b/main/reference/fit_rsp_step.html
index b8de25172c..d06a7ca41e 100644
--- a/main/reference/fit_rsp_step.html
+++ b/main/reference/fit_rsp_step.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -39,37 +39,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/fit_survival_step.html b/main/reference/fit_survival_step.html
index 60c87acd81..7ec1e9e5c8 100644
--- a/main/reference/fit_survival_step.html
+++ b/main/reference/fit_survival_step.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/forest_viewport.html b/main/reference/forest_viewport.html
index b008d2320a..f7e5aa1001 100644
--- a/main/reference/forest_viewport.html
+++ b/main/reference/forest_viewport.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_auto.html b/main/reference/format_auto.html
index 39137d8875..df8dfde6ec 100644
--- a/main/reference/format_auto.html
+++ b/main/reference/format_auto.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_count_fraction.html b/main/reference/format_count_fraction.html
index d146118617..6f928460f7 100644
--- a/main/reference/format_count_fraction.html
+++ b/main/reference/format_count_fraction.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_count_fraction_fixed_dp.html b/main/reference/format_count_fraction_fixed_dp.html
index f674dc0194..b64b672c56 100644
--- a/main/reference/format_count_fraction_fixed_dp.html
+++ b/main/reference/format_count_fraction_fixed_dp.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_count_fraction_lt10.html b/main/reference/format_count_fraction_lt10.html
index 118b9c6a66..3560fb260d 100644
--- a/main/reference/format_count_fraction_lt10.html
+++ b/main/reference/format_count_fraction_lt10.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/format_extreme_values.html b/main/reference/format_extreme_values.html
index c24a8b4d22..3d87b91265 100644
--- a/main/reference/format_extreme_values.html
+++ b/main/reference/format_extreme_values.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_extreme_values_ci.html b/main/reference/format_extreme_values_ci.html
index 997ff0ddd2..abc25cf5f3 100644
--- a/main/reference/format_extreme_values_ci.html
+++ b/main/reference/format_extreme_values_ci.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_fraction.html b/main/reference/format_fraction.html
index 4c1781dd9b..d3282fd40b 100644
--- a/main/reference/format_fraction.html
+++ b/main/reference/format_fraction.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/format_fraction_fixed_dp.html b/main/reference/format_fraction_fixed_dp.html
index 3f8836d277..54b7c03955 100644
--- a/main/reference/format_fraction_fixed_dp.html
+++ b/main/reference/format_fraction_fixed_dp.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/format_fraction_threshold.html b/main/reference/format_fraction_threshold.html
index 18d6662cb1..c6ab3bca6e 100644
--- a/main/reference/format_fraction_threshold.html
+++ b/main/reference/format_fraction_threshold.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -29,37 +29,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/format_sigfig.html b/main/reference/format_sigfig.html
index af819eddf0..8211e5c048 100644
--- a/main/reference/format_sigfig.html
+++ b/main/reference/format_sigfig.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/format_xx.html b/main/reference/format_xx.html
index 475cd0467f..8c54b7186c 100644
--- a/main/reference/format_xx.html
+++ b/main/reference/format_xx.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/formatting_functions.html b/main/reference/formatting_functions.html
index bf7ea657ad..5ed94dcc93 100644
--- a/main/reference/formatting_functions.html
+++ b/main/reference/formatting_functions.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/g_bland_altman.html b/main/reference/g_bland_altman.html
index f3f7edd92f..f3bcf134f7 100644
--- a/main/reference/g_bland_altman.html
+++ b/main/reference/g_bland_altman.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/g_forest.html b/main/reference/g_forest.html
index ff966ea871..d6b9f81d65 100644
--- a/main/reference/g_forest.html
+++ b/main/reference/g_forest.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/g_ipp.html b/main/reference/g_ipp.html
index f6552e9e02..1404e991c8 100644
--- a/main/reference/g_ipp.html
+++ b/main/reference/g_ipp.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/g_km.html b/main/reference/g_km.html
index 67f737c8de..07d2aab4ca 100644
--- a/main/reference/g_km.html
+++ b/main/reference/g_km.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/g_lineplot.html b/main/reference/g_lineplot.html
index cad9f3b1b6..11ad9fb0ab 100644
--- a/main/reference/g_lineplot.html
+++ b/main/reference/g_lineplot.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/g_step.html b/main/reference/g_step.html
index c804614ede..fee2f0428e 100644
--- a/main/reference/g_step.html
+++ b/main/reference/g_step.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/g_waterfall.html b/main/reference/g_waterfall.html
index f607c34b5a..49e64e5c8f 100644
--- a/main/reference/g_waterfall.html
+++ b/main/reference/g_waterfall.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/get_covariates.html b/main/reference/get_covariates.html
index 10e00b750f..6084e32a05 100644
--- a/main/reference/get_covariates.html
+++ b/main/reference/get_covariates.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/get_smooths.html b/main/reference/get_smooths.html
index 32b5f3123c..91083cd62f 100644
--- a/main/reference/get_smooths.html
+++ b/main/reference/get_smooths.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/groups_list_to_df.html b/main/reference/groups_list_to_df.html
index b8d9b62157..e12828e511 100644
--- a/main/reference/groups_list_to_df.html
+++ b/main/reference/groups_list_to_df.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_adlb_abnormal_by_worst_grade.html b/main/reference/h_adlb_abnormal_by_worst_grade.html
index cdcdd4b771..b0b3e37804 100644
--- a/main/reference/h_adlb_abnormal_by_worst_grade.html
+++ b/main/reference/h_adlb_abnormal_by_worst_grade.html
@@ -43,7 +43,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -61,37 +61,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_adlb_worsen.html b/main/reference/h_adlb_worsen.html
index 881b0f2745..36faeacfba 100644
--- a/main/reference/h_adlb_worsen.html
+++ b/main/reference/h_adlb_worsen.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
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-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/h_adsl_adlb_merge_using_worst_flag.html b/main/reference/h_adsl_adlb_merge_using_worst_flag.html
index 7914f972f5..f15eeb2e7d 100644
--- a/main/reference/h_adsl_adlb_merge_using_worst_flag.html
+++ b/main/reference/h_adsl_adlb_merge_using_worst_flag.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_ancova.html b/main/reference/h_ancova.html
index cb38e6027a..8c48e8eb70 100644
--- a/main/reference/h_ancova.html
+++ b/main/reference/h_ancova.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/h_append_grade_groups.html b/main/reference/h_append_grade_groups.html
index 6617c0012f..259e054dd8 100644
--- a/main/reference/h_append_grade_groups.html
+++ b/main/reference/h_append_grade_groups.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_col_indices.html b/main/reference/h_col_indices.html
index 5311e26dd1..449ee7a733 100644
--- a/main/reference/h_col_indices.html
+++ b/main/reference/h_col_indices.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_count_cumulative.html b/main/reference/h_count_cumulative.html
index a9382bdc31..b3f0a35776 100644
--- a/main/reference/h_count_cumulative.html
+++ b/main/reference/h_count_cumulative.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_cox_regression.html b/main/reference/h_cox_regression.html
index 9c4e9a5297..5894a217bc 100644
--- a/main/reference/h_cox_regression.html
+++ b/main/reference/h_cox_regression.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/h_data_plot.html b/main/reference/h_data_plot.html
index 0a2600b124..c37ed407a2 100644
--- a/main/reference/h_data_plot.html
+++ b/main/reference/h_data_plot.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,37 +45,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_decompose_gg.html b/main/reference/h_decompose_gg.html
index 8f252aef24..b8bdfe5e70 100644
--- a/main/reference/h_decompose_gg.html
+++ b/main/reference/h_decompose_gg.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_format_row.html b/main/reference/h_format_row.html
index 36b77e9a3c..e5e1b84c5c 100644
--- a/main/reference/h_format_row.html
+++ b/main/reference/h_format_row.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_g_ipp.html b/main/reference/h_g_ipp.html
index 26ca59c1ee..9ded275e9c 100644
--- a/main/reference/h_g_ipp.html
+++ b/main/reference/h_g_ipp.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_ggkm.html b/main/reference/h_ggkm.html
index 5d2c7bdf81..6d2a51abc8 100644
--- a/main/reference/h_ggkm.html
+++ b/main/reference/h_ggkm.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_glm_count.html b/main/reference/h_glm_count.html
index 7c3ee7a712..97b5fd2925 100644
--- a/main/reference/h_glm_count.html
+++ b/main/reference/h_glm_count.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_grob_coxph.html b/main/reference/h_grob_coxph.html
index f21824bbed..48c64dd65b 100644
--- a/main/reference/h_grob_coxph.html
+++ b/main/reference/h_grob_coxph.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_grob_median_surv.html b/main/reference/h_grob_median_surv.html
index f1f96b4d25..eb92f5e8ac 100644
--- a/main/reference/h_grob_median_surv.html
+++ b/main/reference/h_grob_median_surv.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_grob_tbl_at_risk.html b/main/reference/h_grob_tbl_at_risk.html
index a969c753c1..bb7a3abeeb 100644
--- a/main/reference/h_grob_tbl_at_risk.html
+++ b/main/reference/h_grob_tbl_at_risk.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_grob_y_annot.html b/main/reference/h_grob_y_annot.html
index d403d11236..e37f691079 100644
--- a/main/reference/h_grob_y_annot.html
+++ b/main/reference/h_grob_y_annot.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
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diff --git a/main/reference/h_incidence_rate.html b/main/reference/h_incidence_rate.html
index da1e16e8e3..e6db614ce4 100644
--- a/main/reference/h_incidence_rate.html
+++ b/main/reference/h_incidence_rate.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -25,37 +25,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/h_km_layout.html b/main/reference/h_km_layout.html
index da406ef720..7cec68444a 100644
--- a/main/reference/h_km_layout.html
+++ b/main/reference/h_km_layout.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -27,37 +27,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_logistic_regression.html b/main/reference/h_logistic_regression.html
index 2202e0b8ee..3760fc33c2 100644
--- a/main/reference/h_logistic_regression.html
+++ b/main/reference/h_logistic_regression.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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diff --git a/main/reference/h_map_for_count_abnormal.html b/main/reference/h_map_for_count_abnormal.html
index 506b00a4f9..3dfd455d1c 100644
--- a/main/reference/h_map_for_count_abnormal.html
+++ b/main/reference/h_map_for_count_abnormal.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -29,37 +29,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_odds_ratio.html b/main/reference/h_odds_ratio.html
index 5cbac2ac4e..8da728703e 100644
--- a/main/reference/h_odds_ratio.html
+++ b/main/reference/h_odds_ratio.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_pkparam_sort.html b/main/reference/h_pkparam_sort.html
index 873ef61de4..a9ae75dd93 100644
--- a/main/reference/h_pkparam_sort.html
+++ b/main/reference/h_pkparam_sort.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_ppmeans.html b/main/reference/h_ppmeans.html
index b640b722ea..e4f8c0013e 100644
--- a/main/reference/h_ppmeans.html
+++ b/main/reference/h_ppmeans.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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-<!-- end dropdown for versions -->
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diff --git a/main/reference/h_prop_diff.html b/main/reference/h_prop_diff.html
index afaa58b093..1c3971426c 100644
--- a/main/reference/h_prop_diff.html
+++ b/main/reference/h_prop_diff.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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diff --git a/main/reference/h_prop_diff_test.html b/main/reference/h_prop_diff_test.html
index 122305c833..3dcce07d0c 100644
--- a/main/reference/h_prop_diff_test.html
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@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -25,37 +25,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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diff --git a/main/reference/h_proportions.html b/main/reference/h_proportions.html
index 9352a92026..416d4429cd 100644
--- a/main/reference/h_proportions.html
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@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_response_biomarkers_subgroups.html b/main/reference/h_response_biomarkers_subgroups.html
index e72b6df7a0..76eda3477f 100644
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@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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diff --git a/main/reference/h_response_subgroups.html b/main/reference/h_response_subgroups.html
index b96068c031..75ad0ac580 100644
--- a/main/reference/h_response_subgroups.html
+++ b/main/reference/h_response_subgroups.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_split_by_subgroups.html b/main/reference/h_split_by_subgroups.html
index 1489c383be..606bfaa180 100644
--- a/main/reference/h_split_by_subgroups.html
+++ b/main/reference/h_split_by_subgroups.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/h_split_param.html b/main/reference/h_split_param.html
index 71d93b22ed..5ebb99c408 100644
--- a/main/reference/h_split_param.html
+++ b/main/reference/h_split_param.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/h_stack_by_baskets.html b/main/reference/h_stack_by_baskets.html
index 3bbff77b90..ea9cfa2e2d 100644
--- a/main/reference/h_stack_by_baskets.html
+++ b/main/reference/h_stack_by_baskets.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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diff --git a/main/reference/h_step.html b/main/reference/h_step.html
index 7a8378c27c..de8a464f72 100644
--- a/main/reference/h_step.html
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@@ -9,7 +9,7 @@
 
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@@ -27,37 +27,6 @@
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diff --git a/main/reference/h_survival_biomarkers_subgroups.html b/main/reference/h_survival_biomarkers_subgroups.html
index 5588955852..5c70d7d179 100644
--- a/main/reference/h_survival_biomarkers_subgroups.html
+++ b/main/reference/h_survival_biomarkers_subgroups.html
@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -29,37 +29,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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diff --git a/main/reference/h_survival_duration_subgroups.html b/main/reference/h_survival_duration_subgroups.html
index a7f23efbca..9c59dba74f 100644
--- a/main/reference/h_survival_duration_subgroups.html
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@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -29,37 +29,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/h_tab_one_biomarker.html b/main/reference/h_tab_one_biomarker.html
index 1d11ce5485..9861ed3ec6 100644
--- a/main/reference/h_tab_one_biomarker.html
+++ b/main/reference/h_tab_one_biomarker.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -29,37 +29,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
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diff --git a/main/reference/h_tbl_coxph_pairwise.html b/main/reference/h_tbl_coxph_pairwise.html
index 398b10b35b..445cb663bb 100644
--- a/main/reference/h_tbl_coxph_pairwise.html
+++ b/main/reference/h_tbl_coxph_pairwise.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/h_tbl_median_surv.html b/main/reference/h_tbl_median_surv.html
index 646cb87013..70243d5578 100644
--- a/main/reference/h_tbl_median_surv.html
+++ b/main/reference/h_tbl_median_surv.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/h_worsen_counter.html b/main/reference/h_worsen_counter.html
index a7afefdb3c..4807eae419 100644
--- a/main/reference/h_worsen_counter.html
+++ b/main/reference/h_worsen_counter.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/h_xticks.html b/main/reference/h_xticks.html
index bc4bd964c2..9e8d4b7955 100644
--- a/main/reference/h_xticks.html
+++ b/main/reference/h_xticks.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/imputation_rule.html b/main/reference/imputation_rule.html
index 9d416d5f6d..b4dc0ce205 100644
--- a/main/reference/imputation_rule.html
+++ b/main/reference/imputation_rule.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/incidence_rate.html b/main/reference/incidence_rate.html
index 6003a13118..c0703f666b 100644
--- a/main/reference/incidence_rate.html
+++ b/main/reference/incidence_rate.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -207,8 +176,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("estimate_incidence_rate")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/index.html b/main/reference/index.html
index 2886892047..187d208c2a 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/labels_or_names.html b/main/reference/labels_or_names.html
index af000ff315..2dbc6775df 100644
--- a/main/reference/labels_or_names.html
+++ b/main/reference/labels_or_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/labels_use_control.html b/main/reference/labels_use_control.html
index 052c6f2137..12855e85b0 100644
--- a/main/reference/labels_use_control.html
+++ b/main/reference/labels_use_control.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/logistic_regression_cols.html b/main/reference/logistic_regression_cols.html
index 8ce290d630..120859440a 100644
--- a/main/reference/logistic_regression_cols.html
+++ b/main/reference/logistic_regression_cols.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/logistic_summary_by_flag.html b/main/reference/logistic_summary_by_flag.html
index 1ce4c1a8e3..ed548f7df8 100644
--- a/main/reference/logistic_summary_by_flag.html
+++ b/main/reference/logistic_summary_by_flag.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/make_names.html b/main/reference/make_names.html
index 940c7ecd20..3f11e89d34 100644
--- a/main/reference/make_names.html
+++ b/main/reference/make_names.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/month2day.html b/main/reference/month2day.html
index aeba1a2cef..87a3539940 100644
--- a/main/reference/month2day.html
+++ b/main/reference/month2day.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/muffled_car_anova.html b/main/reference/muffled_car_anova.html
index b3b429248c..72ef12f527 100644
--- a/main/reference/muffled_car_anova.html
+++ b/main/reference/muffled_car_anova.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/n_available.html b/main/reference/n_available.html
index efb5088b9d..782a6a86bf 100644
--- a/main/reference/n_available.html
+++ b/main/reference/n_available.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/odds_ratio.html b/main/reference/odds_ratio.html
index cd595268a9..1d3dbb3475 100644
--- a/main/reference/odds_ratio.html
+++ b/main/reference/odds_ratio.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -194,8 +163,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("estimate_odds_ratio")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'or_ci', 'n_tot'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/prop_diff.html b/main/reference/prop_diff.html
index db30f75f1f..2cc6b3ac0e 100644
--- a/main/reference/prop_diff.html
+++ b/main/reference/prop_diff.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -199,8 +168,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("estimate_proportion_diff")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'diff', 'diff_ci'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/prop_diff_test.html b/main/reference/prop_diff_test.html
index da108c70e1..74b52ffcd8 100644
--- a/main/reference/prop_diff_test.html
+++ b/main/reference/prop_diff_test.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -179,8 +148,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("test_proportion_diff")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pval'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/prune_occurrences.html b/main/reference/prune_occurrences.html
index 9290220514..820f6a7f6e 100644
--- a/main/reference/prune_occurrences.html
+++ b/main/reference/prune_occurrences.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/range_noinf.html b/main/reference/range_noinf.html
index 8f66045dcf..94ee318a53 100644
--- a/main/reference/range_noinf.html
+++ b/main/reference/range_noinf.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/reapply_varlabels.html b/main/reference/reapply_varlabels.html
index 6c1b5ae521..8b5b974bcd 100644
--- a/main/reference/reapply_varlabels.html
+++ b/main/reference/reapply_varlabels.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/response_biomarkers_subgroups.html b/main/reference/response_biomarkers_subgroups.html
index e4cf4c3a1b..d22f9afda7 100644
--- a/main/reference/response_biomarkers_subgroups.html
+++ b/main/reference/response_biomarkers_subgroups.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/response_subgroups.html b/main/reference/response_subgroups.html
index adc0fbe0cc..c180c7bf3f 100644
--- a/main/reference/response_subgroups.html
+++ b/main/reference/response_subgroups.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/rtable2gg.html b/main/reference/rtable2gg.html
index 192c62e6bb..6c6bcab85d 100644
--- a/main/reference/rtable2gg.html
+++ b/main/reference/rtable2gg.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/rtables_access.html b/main/reference/rtables_access.html
index 85260375b5..7aee1540e0 100644
--- a/main/reference/rtables_access.html
+++ b/main/reference/rtables_access.html
@@ -13,7 +13,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -31,37 +31,6 @@
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/s_bland_altman.html b/main/reference/s_bland_altman.html
index 374e7b21fd..ef63ce4869 100644
--- a/main/reference/s_bland_altman.html
+++ b/main/reference/s_bland_altman.html
@@ -11,7 +11,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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diff --git a/main/reference/s_cox_multivariate.html b/main/reference/s_cox_multivariate.html
index ebe6ba4857..b3e1b2244e 100644
--- a/main/reference/s_cox_multivariate.html
+++ b/main/reference/s_cox_multivariate.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -39,37 +39,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/sas_na.html b/main/reference/sas_na.html
index 90d39025ca..271bfaf57a 100644
--- a/main/reference/sas_na.html
+++ b/main/reference/sas_na.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/score_occurrences.html b/main/reference/score_occurrences.html
index b4ec8ce699..57b9d775ee 100644
--- a/main/reference/score_occurrences.html
+++ b/main/reference/score_occurrences.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/split_cols_by_groups.html b/main/reference/split_cols_by_groups.html
index 2d365567bc..633bab81f1 100644
--- a/main/reference/split_cols_by_groups.html
+++ b/main/reference/split_cols_by_groups.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/split_text_grob.html b/main/reference/split_text_grob.html
index b8669f660e..237b27a29b 100644
--- a/main/reference/split_text_grob.html
+++ b/main/reference/split_text_grob.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/stack_grobs.html b/main/reference/stack_grobs.html
index ffcc7e709b..051af19a10 100644
--- a/main/reference/stack_grobs.html
+++ b/main/reference/stack_grobs.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
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 <li class="nav-item dropdown">
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/stat_mean_ci.html b/main/reference/stat_mean_ci.html
index d92acf69fa..f33db099b7 100644
--- a/main/reference/stat_mean_ci.html
+++ b/main/reference/stat_mean_ci.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/stat_mean_pval.html b/main/reference/stat_mean_pval.html
index 0d5ecdfcc1..72b63918cb 100644
--- a/main/reference/stat_mean_pval.html
+++ b/main/reference/stat_mean_pval.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/stat_median_ci.html b/main/reference/stat_median_ci.html
index 553ea5cc83..47149778a2 100644
--- a/main/reference/stat_median_ci.html
+++ b/main/reference/stat_median_ci.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/stat_propdiff_ci.html b/main/reference/stat_propdiff_ci.html
index 0d214df40f..fc2ba5210c 100644
--- a/main/reference/stat_propdiff_ci.html
+++ b/main/reference/stat_propdiff_ci.html
@@ -13,7 +13,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
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diff --git a/main/reference/strata_normal_quantile.html b/main/reference/strata_normal_quantile.html
index a4d206076b..cbcf21b1f1 100644
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@@ -13,7 +13,7 @@
 
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
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diff --git a/main/reference/study_arm.html b/main/reference/study_arm.html
index f6bb97e7c0..242ea33d5f 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -25,37 +25,6 @@
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-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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diff --git a/main/reference/summarize_ancova.html b/main/reference/summarize_ancova.html
index 9fbc4eebbb..90c5a6e051 100644
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+++ b/main/reference/summarize_ancova.html
@@ -23,7 +23,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -41,37 +41,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
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@@ -212,8 +181,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("summarize_ancova")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/summarize_change.html b/main/reference/summarize_change.html
index 330f2001c2..7da89268b7 100644
--- a/main/reference/summarize_change.html
+++ b/main/reference/summarize_change.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -39,37 +39,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -158,8 +127,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("analyze_vars_numeric)</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/summarize_colvars.html b/main/reference/summarize_colvars.html
index 20cee0d299..f42d2b16f9 100644
--- a/main/reference/summarize_colvars.html
+++ b/main/reference/summarize_colvars.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/summarize_functions.html b/main/reference/summarize_functions.html
index cf53450a51..cf2934f85d 100644
--- a/main/reference/summarize_functions.html
+++ b/main/reference/summarize_functions.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/summarize_glm_count.html b/main/reference/summarize_glm_count.html
index dfab87ebcf..0010751bf6 100644
--- a/main/reference/summarize_glm_count.html
+++ b/main/reference/summarize_glm_count.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -209,8 +178,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("summarize_glm_count")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/summarize_logistic.html b/main/reference/summarize_logistic.html
index 7f931c7731..082f066587 100644
--- a/main/reference/summarize_logistic.html
+++ b/main/reference/summarize_logistic.html
@@ -25,7 +25,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -43,37 +43,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/summarize_num_patients.html b/main/reference/summarize_num_patients.html
index e970ee5ab0..8392523ad6 100644
--- a/main/reference/summarize_num_patients.html
+++ b/main/reference/summarize_num_patients.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -41,37 +41,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -196,8 +165,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("summarize_num_patients")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'unique', 'nonunique', 'unique_count'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/summarize_patients_exposure_in_cols.html b/main/reference/summarize_patients_exposure_in_cols.html
index c896f513f0..94a9a02817 100644
--- a/main/reference/summarize_patients_exposure_in_cols.html
+++ b/main/reference/summarize_patients_exposure_in_cols.html
@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,37 +49,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -212,8 +181,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run
-<code>get_stats("analyze_patients_exposure_in_cols")</code> to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'n_patients', 'sum_exposure'</code></p></dd>
 
 
 <dt id="arg--labels">.labels<a class="anchor" aria-label="anchor" href="#arg--labels"></a></dt>
diff --git a/main/reference/survival_biomarkers_subgroups.html b/main/reference/survival_biomarkers_subgroups.html
index a597ffef66..37785cc35a 100644
--- a/main/reference/survival_biomarkers_subgroups.html
+++ b/main/reference/survival_biomarkers_subgroups.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/survival_coxph_pairwise.html b/main/reference/survival_coxph_pairwise.html
index 648440cd2a..b228496dd0 100644
--- a/main/reference/survival_coxph_pairwise.html
+++ b/main/reference/survival_coxph_pairwise.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -189,8 +158,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("coxph_pairwise")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/survival_duration_subgroups.html b/main/reference/survival_duration_subgroups.html
index 2dde228535..6ab1888e01 100644
--- a/main/reference/survival_duration_subgroups.html
+++ b/main/reference/survival_duration_subgroups.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,37 +35,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/survival_time.html b/main/reference/survival_time.html
index 84ee22065b..a45cca3c70 100644
--- a/main/reference/survival_time.html
+++ b/main/reference/survival_time.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,37 +33,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -188,8 +157,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("surv_time")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'median', 'median_ci', 'quantiles', 'range_censor', 'range_event', 'range'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/survival_timepoint.html b/main/reference/survival_timepoint.html
index 752dd85de9..e400ee3181 100644
--- a/main/reference/survival_timepoint.html
+++ b/main/reference/survival_timepoint.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,37 +37,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
@@ -223,8 +192,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt id="arg--stats">.stats<a class="anchor" aria-label="anchor" href="#arg--stats"></a></dt>
-<dd><p>(<code>character</code>)<br> statistics to select for the table. Run <code>get_stats("surv_timepoint")</code>
-to see available statistics for this function.</p></dd>
+<dd><p>(<code>character</code>)<br> statistics to select for the table.</p>
+<p>Options are: <code>'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval'</code></p></dd>
 
 
 <dt id="arg--formats">.formats<a class="anchor" aria-label="anchor" href="#arg--formats"></a></dt>
diff --git a/main/reference/tern-package.html b/main/reference/tern-package.html
index e5146e2007..f9c8d072f2 100644
--- a/main/reference/tern-package.html
+++ b/main/reference/tern-package.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tidy.glm.html b/main/reference/tidy.glm.html
index 1fd1f51efd..833f738fbc 100644
--- a/main/reference/tidy.glm.html
+++ b/main/reference/tidy.glm.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/tidy.step.html b/main/reference/tidy.step.html
index a5d702fbc2..40a21270f0 100644
--- a/main/reference/tidy.step.html
+++ b/main/reference/tidy.step.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,37 +27,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
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diff --git a/main/reference/tidy_coxreg.html b/main/reference/tidy_coxreg.html
index c43676f3e4..d589bf233f 100644
--- a/main/reference/tidy_coxreg.html
+++ b/main/reference/tidy_coxreg.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
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@@ -25,37 +25,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
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diff --git a/main/reference/to_n.html b/main/reference/to_n.html
index d0e8f29862..8991e27d90 100644
--- a/main/reference/to_n.html
+++ b/main/reference/to_n.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -27,37 +27,6 @@
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/to_string_matrix.html b/main/reference/to_string_matrix.html
index 536328b0ee..00aa243ef7 100644
--- a/main/reference/to_string_matrix.html
+++ b/main/reference/to_string_matrix.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -33,37 +33,6 @@
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-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/try_car_anova.html b/main/reference/try_car_anova.html
index dda2b448c3..d91507b887 100644
--- a/main/reference/try_car_anova.html
+++ b/main/reference/try_car_anova.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -25,37 +25,6 @@
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 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
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-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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diff --git a/main/reference/ungroup_stats.html b/main/reference/ungroup_stats.html
index 333ed6994e..cccc640346 100644
--- a/main/reference/ungroup_stats.html
+++ b/main/reference/ungroup_stats.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
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-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
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     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/univariate.html b/main/reference/univariate.html
index 0ff67e03a0..4747bd301d 100644
--- a/main/reference/univariate.html
+++ b/main/reference/univariate.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,37 +29,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
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diff --git a/main/reference/unlist_and_blank_na.html b/main/reference/unlist_and_blank_na.html
index 5a9e7c5f5f..18a077a47c 100644
--- a/main/reference/unlist_and_blank_na.html
+++ b/main/reference/unlist_and_blank_na.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -25,37 +25,6 @@
   </ul></li>
 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4">v0.8.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2">v0.8.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.1">v0.8.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.0">v0.8.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.9">v0.7.9</a> </div></li>
-<!-- end dropdown for versions -->
   <button class="nav-link dropdown-toggle" type="button" id="dropdown-reports" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Reports</button>
   <ul class="dropdown-menu" aria-labelledby="dropdown-reports"><li><a class="dropdown-item" href="../coverage-report/">Coverage report</a></li>
     <li><a class="dropdown-item" href="../unit-test-report/">Unit test report</a></li>
diff --git a/main/reference/update_weights_strat_wilson.html b/main/reference/update_weights_strat_wilson.html
index 633132d866..1b7dc755c8 100644
--- a/main/reference/update_weights_strat_wilson.html
+++ b/main/reference/update_weights_strat_wilson.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">tern</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9005</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.9.6.9006</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,37 +31,6 @@
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 <li class="nav-item"><a class="nav-link" href="../news/index.html">Changelog</a></li>
 <li class="nav-item dropdown">
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/release-candidate">release-candidate</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2-rc1">v0.9.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1-rc3">v0.9.1-rc3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc2">v0.8.5-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5-rc1">v0.8.5-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.4-rc1">v0.8.4-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc2">v0.8.3-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.3-rc1">v0.8.3-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc2">v0.8.2-rc2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.2-rc1">v0.8.2-rc1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.7.10">v0.7.10</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.6">v0.9.6</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.5">v0.9.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.4">v0.9.4</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.3">v0.9.3</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.2">v0.9.2</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.1">v0.9.1</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.9.0">v0.9.0</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/tern/v0.8.5">v0.8.5</a>
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-[{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/tern/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"variable-class-conversion","dir":"Articles","previous_headings":"","what":"Variable Class Conversion","title":"Missing Values in Tern","text":"rtables requires split variables factors. try split variable isn’t, warning message appear. purposefully convert SEX variable character demonstrate happens try splitting rows variable. fix , df_explict_na convert factor resulting table generated.","code":"adsl <- tern_ex_adsl adsl$SEX <- as.character(adsl$SEX)  vars <- c(\"AGE\", \"SEX\", \"RACE\", \"BMRKR1\") var_labels <- c(   \"Age (yr)\",   \"Sex\",   \"Race\",   \"Continous Level Biomarker 1\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures result #>                                                A: Drug X    B: Placebo    C: Combination   All Patients #>                                                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                                                #>   n                                               69            73              58             200      #>   Mean (SD)                                   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median                                         32.8          35.4            36.2            34.8     #>   Min - Max                                   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                                                     #>   n                                               69            73              58             200      #>   F                                           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                                           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)   #> Race                                                                                                    #>   n                                               69            73              58             200      #>   ASIAN                                       38 (55.1%)    43 (58.9%)       29 (50%)       110 (55%)   #>   BLACK OR AFRICAN AMERICAN                   15 (21.7%)    13 (17.8%)      12 (20.7%)       40 (20%)   #>   WHITE                                       11 (15.9%)    12 (16.4%)       11 (19%)        34 (17%)   #>   AMERICAN INDIAN OR ALASKA NATIVE             4 (5.8%)      3 (4.1%)       6 (10.3%)       13 (6.5%)   #>   MULTIPLE                                     1 (1.4%)      1 (1.4%)           0             2 (1%)    #>   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         1 (1.4%)           0            1 (0.5%)   #>   OTHER                                            0             0              0               0       #>   UNKNOWN                                          0             0              0               0       #> Continous Level Biomarker 1                                                                             #>   n                                               69            73              58             200      #>   Mean (SD)                                    6.3 (3.6)     6.7 (3.5)      6.2 (3.3)       6.4 (3.5)   #>   Median                                          5.4           6.3            5.4             5.6      #>   Min - Max                                   0.4 - 17.8    1.0 - 18.5      2.4 - 19.1      0.4 - 19.1"},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"including-missing-values-in-rtables","dir":"Articles","previous_headings":"","what":"Including Missing Values in rtables","title":"Missing Values in Tern","text":"purposefully convert M values NA SEX variable. running df_explicit_na NA values encoded <Missing> included table. well, missing values included n count included denominator value calculating percent values. want Na values displayed table included n count denominator calculating percent values, use na_level argument.","code":"adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               69            73              58             200      #>   Mean (SD)   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median         32.8          35.4            36.2            34.8     #>   Min - Max   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                     #>   n               38            40              32             110      #>   F            38 (100%)     40 (100%)      32 (100%)       110 (100%)  #>   M                0             0              0               0 adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                     A: Drug X    B: Placebo    C: Combination   All Patients #>                      (N=69)        (N=73)          (N=58)         (N=200)    #> ———————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                     #>   n                    69            73              58             200      #>   Mean (SD)        34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median              32.8          35.4            36.2            34.8     #>   Min - Max        22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                          #>   n                    69            73              58             200      #>   F                38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                     0             0              0               0       #>   Missing Values   31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/missing_values.html","id":"missing-values-in-numeric-variables","dir":"Articles","previous_headings":"","what":"Missing Values in Numeric Variables","title":"Missing Values in Tern","text":"Numeric variables missing values altered. means NA value numeric variable included summary statistics, included denominator value calculating percent values. make value less 30 missing AGE variable valued greater 30 included table .","code":"adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               46            56              44             146      #>   Mean (SD)   37.8 (5.2)    38.3 (6.3)      39.1 (5.9)      38.3 (5.8)  #>   Median         37.2          37.3            37.5            37.5     #>   Min - Max   30.3 - 48.0   30.0 - 57.5    30.5 - 58.3     30.0 - 58.3  #> Sex                                                                     #>   n               69            73              58             200      #>   F           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tern-tabulation","dir":"Articles","previous_headings":"","what":"tern Tabulation","title":"Tabulation","text":"tern R package provides functions create common analyses clinical trials R. core functionality tabulation built general purpose rtables package. New users first begin reading “Introduction tern” “Introduction rtables” vignettes. packages used vignette : datasets used vignette :","code":"library(rtables) library(tern) library(dplyr) adsl <- ex_adsl adae <- ex_adae adrs <- ex_adrs"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tern-analyze-functions","dir":"Articles","previous_headings":"","what":"tern Analyze Functions","title":"Tabulation","text":"Analyze functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analyze functions wrappers around rtables::analyze function, offer various methods useful perspective clinical trials statistical projects. Examples tern analyze functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analyze functions recommended use tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"internals-of-tern-analyze-functions","dir":"Articles","previous_headings":"tern Analyze Functions","what":"Internals of tern Analyze Functions","title":"Tabulation","text":"Please skip subsection interested internals tern analyze functions. Internally tern analyze functions like summarize_ancova mainly built 4 elements chain: descriptions function type: analysis helper functions h_*. functions useful help define analysis. statistics function s_*. Statistics functions computation numbers tabulated later. order separate computation formatting, take care rcell type formatting . formatted analysis functions a_*. arguments corresponding statistics functions, can customized calling rtables::make_afun() . used afun rtables::analyze(). analyze functions rtables::analyze(..., afun = make_afun(tern::a_*)). Analyze functions used combination rtables layout functions, pipeline creates table. last element chain. use native rtables::analyze function tern formatted analysis functions afun parameter. rtables::make_afun function helpful somebody wants attach format formatted analysis function.","code":"h_ancova() -> tern:::s_ancova() -> tern:::a_ancova() -> summarize_ancova() l <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = a_summary)  build_table(l, df = adrs) afun <- make_afun(     a_summary,     .stats = NULL,     .formats = c(median = \"xx.\"),     .labels = c(median = \"My median\"),     .indent_mods = c(median = 1L) )  l2 <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = afun)  build_table(l2, df = adrs)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"tabulation-examples","dir":"Articles","previous_headings":"","what":"Tabulation Examples","title":"Tabulation","text":"going create 3 different tables using tern analyze functions rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"demographic-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Demographic Table","title":"Tabulation","text":"Demographic tables provide summary characteristics patients enrolled clinical trial. Typically table columns represent treatment arms variables summarized table demographic properties age, sex, race, etc. example function tern analyze_vars() remaining layout functions rtables. change display order categorical variables table use factor variables explicitly set order levels. case display order columns rows. Note forcats package many useful functions help types data processing steps (used ). tern package includes many functions similar analyze_vars(). functions called layout creating functions used combination rtables layout functions just like examples . Layout creating functions wrapping calls rtables analyze(), analyze_colvars() summarize_row_groups() provide options easy formatting analysis modifications. customize display demographics table, can via arguments analyze_vars(). layout creating functions tern include standard arguments .stats, .formats, .labels .indent_mods control statistics displayed numbers formatted. Refer package help help(\"analyze_vars\") ?analyze_vars see full set options. example change default summary numeric variables include number records, mean standard deviation (single statistic, .e. within single cell). categorical variables modify summary include number records counts categories. also modify display format mean standard deviation print two decimal places instead just one. One feature layout can used different datasets create different summaries. example, can easily create summary demographics Brazil China subgroups, respectively:","code":"# Select variables to include in table. vars <- c(\"AGE\", \"SEX\") var_labels <- c(\"Age (yr)\", \"Sex\")  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                       A: Drug X    B: Placebo    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          33.8 (6.6)    35.4 (7.9)      35.4 (7.7)      34.9 (7.4)  #>   Median                33.0          35.0            35.0            34.0     #>   Min - Max          21.0 - 50.0   21.0 - 62.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   F                   79 (59%)     77 (57.5%)       66 (50%)      222 (55.5%)  #>   M                  51 (38.1%)     55 (41%)       60 (45.5%)     166 (41.5%)  #>   U                   3 (2.2%)      2 (1.5%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED    1 (0.7%)          0           2 (1.5%)        3 (0.8%) # Reorder the levels in the ARM variable. adsl$ARM <- factor(adsl$ARM, levels = c(\"B: Placebo\", \"A: Drug X\", \"C: Combination\"))  # Reorder the levels in the SEX variable. adsl$SEX <- factor(adsl$SEX, levels = c(\"M\", \"F\", \"U\", \"UNDIFFERENTIATED\"))  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          35.4 (7.9)    33.8 (6.6)      35.4 (7.7)      34.9 (7.4)  #>   Median                35.0          33.0            35.0            34.0     #>   Min - Max          21.0 - 62.0   21.0 - 50.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   M                   55 (41%)     51 (38.1%)      60 (45.5%)     166 (41.5%)  #>   F                  77 (57.5%)     79 (59%)        66 (50%)      222 (55.5%)  #>   U                   2 (1.5%)      3 (2.2%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED        0         1 (0.7%)        2 (1.5%)        3 (0.8%) # Select statistics and modify default formats. basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels,     .stats = c(\"n\", \"mean_sd\", \"count\"),     .formats = c(mean_sd = \"xx.xx (xx.xx)\")   ) %>%   build_table(adsl) #>                       B: Placebo     A: Drug X     C: Combination   All Patients #>                        (N=134)        (N=134)         (N=132)         (N=400)    #> ———————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                         #>   n                      134            134             132             400      #>   Mean (SD)          35.43 (7.90)   33.77 (6.55)    35.43 (7.72)    34.88 (7.44) #> Sex                                                                              #>   n                      134            134             132             400      #>   M                       55             51              60             166      #>   F                       77             79              66             222      #>   U                       2              3               4               9       #>   UNDIFFERENTIATED        0              1               2               3 lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   )  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"BRA\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                         (N=7)        (N=13)          (N=10)          (N=30)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                       7            13              10              30      #>   Mean (SD)          32.0 (6.1)    36.7 (6.4)     38.3 (10.6)      36.1 (8.1)  #>   Median                32.0          37.0            35.0            35.5     #>   Min - Max          25.0 - 42.0   24.0 - 47.0    25.0 - 64.0     24.0 - 64.0  #> Sex                                                                            #>   n                       7            13              10              30      #>   M                   4 (57.1%)     8 (61.5%)       5 (50%)        17 (56.7%)  #>   F                   3 (42.9%)     5 (38.5%)       5 (50%)        13 (43.3%)  #>   U                       0             0              0               0       #>   UNDIFFERENTIATED        0             0              0               0  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"CHN\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=81)        (N=74)          (N=64)         (N=219)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      81            74              64             219      #>   Mean (SD)          35.7 (7.3)    33.0 (6.4)      35.2 (6.4)      34.6 (6.8)  #>   Median                36.0          32.0            35.0            34.0     #>   Min - Max          21.0 - 58.0   23.0 - 48.0    21.0 - 49.0     21.0 - 58.0  #> Sex                                                                            #>   n                      81            74              64             219      #>   M                  35 (43.2%)    27 (36.5%)      30 (46.9%)       92 (42%)   #>   F                  45 (55.6%)    44 (59.5%)      29 (45.3%)     118 (53.9%)  #>   U                   1 (1.2%)      2 (2.7%)        3 (4.7%)        6 (2.7%)   #>   UNDIFFERENTIATED        0         1 (1.4%)        2 (3.1%)        3 (1.4%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"adverse-event-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Adverse Event Table","title":"Tabulation","text":"standard table adverse events summary system organ class preferred term. frequency counts preferred term, multiple occurrences AE individual count . create table need use combination several layout creating functions tabulation pipeline. start creating high-level summary. layout creating function tern can summarize_num_patients(): Note table, denominator used percentages shown header table (N = xx) defined based subject-level dataset adsl. done using alt_df_counts argument build_table(), provides alternative data set deriving counts header. often required work data sets include multiple records per patient df, adae .","code":"basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                  A: Drug X    B: Placebo    C: Combination   All Patients #>                                                   (N=134)       (N=134)        (N=132)         (N=400)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE   122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                      609           622            703             1934"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"statistics-functions","dir":"Articles","previous_headings":"Tabulation Examples > Adverse Event Table","what":"Statistics Functions","title":"Tabulation","text":"building rest AE table helpful introduce tern package design conventions. layout creating function tern wrapper Statistics function. Statistics functions ones actual computation numbers table. functions always return named lists whose elements statistics available include layout via .stats argument layout creating function level. Statistics functions follow naming convention always begin s_* ease use documented page layout creating function counterpart. helpful review Statistic function understand logic used calculate numbers table see options may available modify analysis. example, Statistics function calculating numbers summarize_num_patients() s_num_patients(). results Statistics function list elements unique, nonunique unique_count: results can see unique nonunique statistics displayed “Patients” column initial AE table output . Also can see raw numbers formatted way. formatting functionality handled layout creating function level .formats argument. Now know types statistics can derived s_num_patients(), can try modifying default layout returned summarize_num_patients(). Instead reporting unique nonqunie statistics, specify analysis include unique_count statistic. result show counts unique patients. Note make update .stats .labels argument summarize_num_patients(). Let’s now continue building layout adverse event table. top-level summary, can repeat summary system organ class level. split analysis data split_rows_by() calling summarize_num_patients(). table looks almost ready. final step, need layout creating function can produce count table event frequencies. layout creating function count_occurrences(). Let’s first try using function simpler layout without row splits: Putting everything together, final AE table looks like :","code":"s_num_patients(x = adae$USUBJID, labelstr = \"\", .N_col = nrow(adae)) #> $unique #> [1] 365.000000   0.188728 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 1934 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 365 #> attr(,\"label\") #> [1] \"(n)\" basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\",     .labels = c(unique_count = \"Total number of patients with at least one AE\")   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                 A: Drug X   B: Placebo   C: Combination   All Patients #>                                                  (N=134)     (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE      122         123            120             365 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                 A: Drug X    B: Placebo   C: Combination   All Patients #>                  (N=134)      (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————— #> dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%)  #> dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%)  #> dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%)  #> dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%)  #> dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%)  #> dcd C.1.1.1.3   43 (32.1%)   46 (34.3%)     43 (32.6%)     132 (33.0%)  #> dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%)  #> dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%)  #> dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%)  #> dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #>     dcd A.1.1.1.1                                 50 (37.3%)    45 (33.6%)      63 (47.7%)     158 (39.5%)  #>     dcd A.1.1.1.2                                 48 (35.8%)    48 (35.8%)      50 (37.9%)     146 (36.5%)  #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #>     dcd B.1.1.1.1                                 47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #>     dcd B.2.1.2.1                                 49 (36.6%)    44 (32.8%)      52 (39.4%)     145 (36.2%)  #>     dcd B.2.2.3.1                                 48 (35.8%)    54 (40.3%)      51 (38.6%)     153 (38.2%)  #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #>     dcd C.1.1.1.3                                 43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #>     dcd C.2.1.2.1                                 35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #>     dcd D.1.1.1.1                                 50 (37.3%)    42 (31.3%)      51 (38.6%)     143 (35.8%)  #>     dcd D.1.1.4.2                                 48 (35.8%)    42 (31.3%)      50 (37.9%)     140 (35.0%)  #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208      #>     dcd D.2.1.5.3                                 47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"response-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Response Table","title":"Tabulation","text":"typical response table binary clinical trial endpoint may composed several different analyses: Proportion responders treatment group Difference proportion responders comparison groups vs. control group Chi-Square test difference response rates comparison groups vs. control group can build table layout like following approach used AE table: table section produced using different layout creating function tern. First start data preparation steps set analysis dataset. select endpoint analyze PARAMCD define logical variable is_rsp indicates whether patient classified responder . create summary proportion responders treatment group, use estimate_proportion() layout creating function: specify arm table used reference, use argument ref_group split_cols_by(). change reference arm “B: Placebo” arm displayed first column: customize analysis, can use method conf_level arguments modify type confidence interval calculated: next table section needed summarize difference response rates reference arm comparison arm. Use estimate_proportion_diff() layout creating function : final section needed complete table includes statistical test difference response rates. Use test_proportion_diff() layout creating function : customize output, use method argument select Chi-Squared test Schouten correction. Now can put table sections together one layout pipeline. Note one small change needed. Since primary analysis variable table sections (is_rsp), need give sub-table unique name. done adding table_names argument providing unique names :","code":"# Preprocessing to select an analysis endpoint. anl <- adrs %>%   dplyr::filter(PARAMCD == \"BESRSPI\") %>%   dplyr::mutate(is_rsp = AVALC %in% c(\"CR\", \"PR\")) basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     table_names = \"est_prop\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9   ) %>%   build_table(anl) #>                             A: Drug X      B: Placebo    C: Combination #>                              (N=134)        (N=134)         (N=132)     #> ——————————————————————————————————————————————————————————————————————— #> Responders                 114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)   (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(anl) #>                                       A: Drug X    B: Placebo   C: Combination #>                                        (N=134)      (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————————————— #> Unstratified Analysis                                                          #>   Difference in Response rate (%)       17.9                         23.7      #>     95% CI (Wald, with correction)   (7.2, 28.6)                 (13.7, 33.8) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(vars = \"is_rsp\") %>%   build_table(anl) #>                                A: Drug X   B: Placebo   C: Combination #>                                 (N=134)     (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test)    0.0006                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\"   ) %>%   build_table(anl) #>                                                         A: Drug X   B: Placebo   C: Combination #>                                                          (N=134)     (N=134)        (N=132)     #> ——————————————————————————————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test with Schouten Correction)    0.0008                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9,     table_names = \"est_prop\"   ) %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\",     table_names = \"est_prop_diff\"   ) %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\",     table_names = \"test_prop_diff\"   ) %>%   build_table(anl) #>                                                          A: Drug X      B: Placebo    C: Combination #>                                                           (N=134)        (N=134)         (N=132)     #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> Responders                                              114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)                                (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7)  #> Unstratified Analysis                                                                                #>   Difference in Response rate (%)                           17.9                           23.7      #>     95% CI (Wald, with correction)                      (7.2, 28.6)                    (13.7, 33.8)  #>   p-value (Chi-Squared Test with Schouten Correction)      0.0008                        <0.0001"},{"path":"https://insightsengineering.github.io/tern/main/articles/tables.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Tabulation","text":"Tabulation tern builds top layout tabulation framework rtables. Complex tables built step step pipeline combining layout creating functions perform specific type analysis. tern analyze functions introduced vignette : analyze_vars() summarize_num_patients() count_occurrences() estimate_proportion() estimate_proportion_diff() test_proportion_diff() Layout creating functions build formatted layout controlling features labels, numerical display formats indentation. functions wrappers Statistics functions calculate raw summaries analysis. can easily spot Statistics functions documentation always begin prefix s_. can helpful inspect run Statistics functions understand ways analysis can customized.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"common-clinical-trials-analyses","dir":"Articles","previous_headings":"","what":"Common Clinical Trials Analyses","title":"Introduction to tern","text":"package provides large range functionality create tables graphs used clinical trial statistical analysis. rtables tabulation extended clinical trials specific functions: demographics unique patients exposure across patients change baseline parameters statistical model fits: MMRM, logistic regression, Cox regression, … … rtables tabulation helper functions: pre-processing conversions transformations … data visualizations connected clinical trials: Kaplan-Meier plots forest plots line plots … data visualizations helper functions: arrange/stack multiple graphs embellishing graphs/tables metadata details, adding titles, footnotes, page number, etc. … reference tern functions available tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"analytical-functions-for-rtables","dir":"Articles","previous_headings":"","what":"Analytical Functions for rtables","title":"Introduction to tern","text":"Analytical functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analytical functions wrappers around rtables::analyze function; offer various methods useful perspective clinical trials statistical projects. Examples tern analytical functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analytical functions recommended use reference subsection tern website. rtables code first describe two tables assign descriptions variables lyt lyt2. built tables using actual data rtables::build_table. description table called table layout. analyze instruction adds layout ARM variable analyzed mean analysis function result rounded 1 decimal place. Hence, layout “pre-data”; , ’s description build table get data. Defining table layout pure rtables code: , tern function used analyze_vars replaces rtables::analyze function used . see tern offers advanced analysis extending rtables function calls one additional function call. examples tabulation analyze functions presented Tabulation vignette.","code":"library(tern) library(dplyr) # Create table layout pure rtables lyt <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   rtables::analyze(vars = \"AVAL\", mean, format = \"xx.x\") # Create table layout with tern analyze_vars analyze function lyt2 <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", .formats = c(\"mean_sd\" = \"(xx.xx, xx.xx)\")) # Apply table layout to data and produce `rtables` object  adrs <- formatters::ex_adrs  rtables::build_table(lyt, df = adrs) #>                    A: Drug X   B: Placebo   C: Combination #> —————————————————————————————————————————————————————————— #> SCREENING                                                  #>   mean                3.0         3.0            3.0       #> BASELINE                                                   #>   mean                2.5         2.8            2.5       #> END OF INDUCTION                                           #>   mean                1.7         2.1            1.6       #> FOLLOW UP                                                  #>   mean                2.2         2.9            2.0 rtables::build_table(lyt2, df = adrs) #>                     A: Drug X      B: Placebo    C: Combination #> ——————————————————————————————————————————————————————————————— #> SCREENING                                                       #>   n                    154            178             144       #>   Mean (SD)        (3.00, 0.00)   (3.00, 0.00)    (3.00, 0.00)  #>   Median               3.0            3.0             3.0       #>   Min - Max         3.0 - 3.0      3.0 - 3.0       3.0 - 3.0    #> BASELINE                                                        #>   n                    136            146             124       #>   Mean (SD)        (2.46, 0.88)   (2.77, 1.00)    (2.46, 1.08)  #>   Median               3.0            3.0             3.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> END OF INDUCTION                                                #>   n                    218            205             217       #>   Mean (SD)        (1.75, 0.90)   (2.14, 1.28)    (1.65, 1.06)  #>   Median               2.0            2.0             1.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> FOLLOW UP                                                       #>   n                    164            153             167       #>   Mean (SD)        (2.23, 1.26)   (2.89, 1.29)    (1.97, 1.01)  #>   Median               2.0            4.0             2.0       #>   Min - Max         1.0 - 4.0      1.0 - 4.0       1.0 - 4.0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"clinical-trial-visualizations","dir":"Articles","previous_headings":"","what":"Clinical Trial Visualizations","title":"Introduction to tern","text":"Clinical trial related plots complement rich palette tern tabulation analysis functions. Thus tern package delivers full-featured tool clinical trial reporting. tern plot functions return graphs ggplot2 objects. optional nestcolor package can loaded apply standardized NEST color palette tern plots. Line plot without table generated g_lineplot function.  Line plot table generated g_lineplot function.  tern functions used plot generation g_ prefixed listed tern website functions reference.","code":"adsl <- formatters::ex_adsl adlb <- formatters::ex_adlb adlb <- dplyr::filter(adlb, PARAMCD == \"ALT\", AVISIT != \"SCREENING\") library(nestcolor) # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\") # Mean with CI, table, and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"interactive-apps","dir":"Articles","previous_headings":"","what":"Interactive Apps","title":"Introduction to tern","text":"tern outputs can easily converted shiny apps. recommend building apps using teal package, shiny-based interactive exploration framework analyzing data. variety pre-made teal shiny apps tern outputs available teal.modules.clinical package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to tern","text":"summary, tern contains many additional functions creating tables, listings, graphs used clinical trials statistical analyses. design package gives users flexibility meet analysis needs regulatory exploratory reporting contexts. information please explore tern website.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"tern-formatting-functions-overview","dir":"Articles","previous_headings":"","what":"tern Formatting Functions Overview","title":"Formatting Functions","text":"tern R package provides functions create common analyses clinical trials R functions default formatting arguments displaying values output specific way. tern formatting differs compared formatting available formatters package tern formats capable handling logical statements, allowing fine-tuning output displayed. Depending type value displayed, value , format output change. Whereas using formatters package, specified format applied regardless value. see available formatting functions available tern see ?formatting_functions. see available format strings available formatters see formatters::list_valid_format_labels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"comparing-tern-formatters-formats","dir":"Articles","previous_headings":"","what":"Comparing tern & formatters Formats","title":"Formatting Functions","text":"packages used vignette : example demonstrates use tern formatting count_abnormal() function. example “low” category non-zero numerator value fraction percentage value displayed, “high” value numerator value zero fraction value displayed without also displaying redundant zero percentage value. following example count_abnormal() function utilized . time “low” values “high” values non-zero numerator show percentage. following example demonstrates difference formatters used instead format output. choose use \"xx / xx\" value format. “high” value zero numerator value “low” value non-zero numerator, yet displayed format. concept occurs using available formats formatters package. following example displays result using \"xx.x / xx.x\" format instead. Use formatters::list_valid_format_labels() see full list available formats formatters.","code":"library(rtables) library(formatters) library(tern) library(dplyr) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs   #> ————————————————— #> low    2/2 (100%) #> high      0/2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx / xx\")   ) %>%   build_table(df2) #>        all obs #> —————————————— #> low     2 / 2  #> high    0 / 2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx.x / xx.x\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    2.0 / 2.0 #> high   0.0 / 2.0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"formatting-function-basics","dir":"Articles","previous_headings":"","what":"Formatting Function Basics","title":"Formatting Functions","text":"Current tern formatting functions consider following aspects setting custom behaviors: Missing values - custom value string can set display missing values instead NA. 0’s - cell value zero, tern fraction formatting functions exclude accompanying percentage value. Number decimal places display - number decimal places can fixed needed. Value thresholds - different format value can displayed depending whether value within certain threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"number-of-decimal-places-to-display","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Number of Decimal Places to Display","title":"Formatting Functions","text":"Two functions set fixed number decimal places (specifically 1) format_fraction_fixed_dp() format_count_fraction_fixed_dp(). default, formatting functions remove trailing zeros, two functions always one decimal place percentage, even digit zero. See following example:","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 3L)) #> [1] \"1/3 (33.3%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\"  format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.25)) #> [1] \"2 (25.0%)\""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"value-thresholds","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Value Thresholds","title":"Formatting Functions","text":"Functions set custom values according certain threshold include format_extreme_values(), format_extreme_values_ci(), format_fraction_threshold(). extreme value formats work similarly allow user specify maximum number digits include, large small values given special string value. example: format_fraction_threshold() function allows user specify lower percentage threshold, values instead assigned special string value. example: See documentation function specific details behavior customize .","code":"extreme_format <- format_extreme_values(digits = 2) extreme_format(0.235) #> [1] \"0.23\" extreme_format(0.001) #> [1] \"<0.01\" extreme_format(Inf) #> [1] \">999.99\" fraction_format <- format_fraction_threshold(0.05) fraction_format(x = c(20, 0.1)) #> [1] 10 fraction_format(x = c(2, 0.01)) #> [1] \"<5\""},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"creating-custom-formatting-functions","dir":"Articles","previous_headings":"","what":"Creating Custom Formatting Functions","title":"Formatting Functions","text":"table requires customized output displayed using one pre-existing tern formatting functions, may want consider creating new formatting function. creating formatting function important consider aspects listed Formatting Function Customization section . section create custom formatting function derived format_fraction_fixed_dp() function. First take look function detail customize . see numerator value greater 0, fraction percentage displayed. numerator 0, fraction shown. Percent values always display 1 decimal place. create dummy dataset observe output value behavior formatting function applied. Now modify function make custom formatting function, custom_format. want display 3 decimal places percent value, numerator value 0 want display 0 value (without denominator).","code":"# First we will see how the format_fraction_fixed_dp code works and displays the outputs format_fraction_fixed_dp <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"], \"/\", x[\"denom\"])   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\"     )   }   return(result) } df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction_fixed_dp)   ) %>%   build_table(df2) #>          all obs    #> ——————————————————— #> low    2/2 (100.0%) #> high       0/2 custom_format <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"]) # We remove the denominator on this line so that only a 0 is displayed   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.3f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" # We include 3 decimal places with %.3f     )   }   return(result) }  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = custom_format) # Here we implement our new custom_format function   ) %>%   build_table(df2) #>           all obs     #> ————————————————————— #> low    2/2 (100.000%) #> high         0"},{"path":"https://insightsengineering.github.io/tern/main/articles/tern_formats.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Formatting Functions","text":"tern analysis function pre-specified default format functions implement generating output, taken formatters package custom formatting functions stored tern. tern functions differ compared formatters logical statements can used set value-dependent customized formats. like create custom formatting function use tern, sure carefully consider rules want implement handle different input values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Daniel Sabanés Bové. Author. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Heng Wang. Author. Francois Collin. Author. Adrian Waddell. Author. Pawel Rucki. Author. Chendi Liao. Author. Jennifer Li. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/tern/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Sabanés Bové D, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Wang H, Collin F, Waddell , Rucki P, Liao C, Li J (2024). tern: Create Common TLGs Used Clinical Trials. R package version 0.9.6.9005, https://github.com/insightsengineering/tern/, https://insightsengineering.github.io/tern/main/.","code":"@Manual{,   title = {tern: Create Common TLGs Used in Clinical Trials},   author = {Joe Zhu and Daniel {Sabanés Bové} and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Heng Wang and Francois Collin and Adrian Waddell and Pawel Rucki and Chendi Liao and Jennifer Li},   year = {2024},   note = {R package version 0.9.6.9005,     https://github.com/insightsengineering/tern/},   url = {https://insightsengineering.github.io/tern/main/}, }"},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"tern-","dir":"","previous_headings":"","what":"Create Common TLGs Used in Clinical Trials","title":"Create Common TLGs Used in Clinical Trials","text":"tern R package contains analysis functions create tables graphs used clinical trial reporting. package provides large range functionality, : Data visualizations: Line plots (g_lineplot) Kaplan-Meier plots (g_km) Forest plots (g_forest) STEP graphs (g_step) Individual patient plots (g_ipp) Waterfall plots (g_waterfall) Bland-Altman plots (g_bland_altman) Statistical model fit summaries: Logistic regression (summarize_logistic) Cox regression (summarize_coxreg) Analysis tables: See list available analyze functions See list available summarize functions See list available column-wise analysis functions Many outputs available added teal shiny applications interactive exploration data. teal modules available teal.modules.clinical package. See TLG Catalog extensive catalog example clinical trial tables, listings, graphs created using tern functionality.","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create Common TLGs Used in Clinical Trials","text":"tern available CRAN can install latest released version : can install latest development version directly GitHub running following:","code":"install.packages(\"tern\") # install.packages(\"pak\") pak::pak(\"insightsengineering/tern\")"},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create Common TLGs Used in Clinical Trials","text":"understand use package, please refer Introduction tern article, provides multiple examples code implementation. See package vignettes browseVignettes(package = \"tern\") usage package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"related","dir":"","previous_headings":"","what":"Related","title":"Create Common TLGs Used in Clinical Trials","text":"rtables - table engine used tlg-catalog - website showcasing many examples clinical trial tables, listings, graphs teal.modules.clinical - teal modules interactive data analysis","code":""},{"path":"https://insightsengineering.github.io/tern/main/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"Create Common TLGs Used in Clinical Trials","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal range values — abnormal","title":"Count patients with abnormal range values — abnormal","text":"analyze function count_abnormal() creates layout element count patients abnormal analysis range values direction. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), fraction patient counts returned, numerator denominator calculated follows: num: number patients abnormality recorded treatment. denom: total number patients least one post-baseline assessment. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal range values — abnormal","text":"","code":"count_abnormal(   lyt,   var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )  a_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal range values — abnormal","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (named list) list identifying abnormal range level(s) var. Defaults list(Low = \"LOW\", High = \"HIGH\") can also group different levels named list, example, abnormal = list(Low = c(\"LOW\", \"LOW LOW\"), High = c(\"HIGH\", \"HIGH HIGH\")). variables (named list string) list additional analysis variables. exclude_base_abn (flag) whether exclude subjects baseline abnormality numerator denominator. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"abnormal\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal() table layout. s_count_abnormal() returns statistic fraction vector num denom counts patients. a_count_abnormal() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal(): Statistics function counts patients abnormal range values single abnormal level. a_count_abnormal(): Formatted analysis function used afun count_abnormal().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() considers single variable contains multiple abnormal levels. df filtered include post-baseline records. denominator includes patients may abnormal levels baseline, patients missing baseline records. Patients abnormalities baseline can optionally excluded numerator denominator via exclude_base_abn parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal range values — abnormal","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  df <- data.frame(   USUBJID = as.character(c(1, 1, 2, 2)),   ANRIND = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BNRIND = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df <- df %>%   filter(ONTRTFL == \"Y\")  # Layout creating function. basic_table() %>%   count_abnormal(var = \"ANRIND\", abnormal = list(high = \"HIGH\", low = \"LOW\")) %>%   build_table(df) #>         all obs  #> ———————————————— #> high   1/2 (50%) #> low    1/2 (50%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"analyze function count_abnormal_by_baseline() creates layout element count patients abnormal analysis range values, categorized baseline status. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), condition baseline range result count patients numerator denominator follows following categories: <abnormality> num:  number patients without abnormality baseline (excluding missing baseline) least one abnormality post-baseline. denom: number patients without abnormality baseline (excluding missing baseline). <Abnormality> num: number patients abnormality baseline least one abnormality post-baseline. denom: number patients abnormality baseline. Total num: number patients least one post-baseline record least one abnormality post-baseline. denom: number patients least one post-baseline record. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"count_abnormal_by_baseline(   lyt,   var,   abnormal,   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   na_str = \"<Missing>\",   nested = TRUE,   ...,   table_names = abnormal,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )  a_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (character) values identifying abnormal range level(s) .var. variables (named list string) list additional analysis variables. na_str (string) explicit na_level argument used pre-processing steps (maybe df_explicit_na()). default \"<Missing>\". nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"abnormal_by_baseline\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_baseline() table layout. s_count_abnormal_by_baseline() returns statistic fraction named list 3 labeled elements: not_abnormal, abnormal, total. element contains vector num denom patient counts. a_count_abnormal_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_baseline(): Statistics function single abnormal level. a_count_abnormal_by_baseline(): Formatted analysis function used afun count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"df filtered include post-baseline records. baseline variable analysis variable contains NA records, expected df pre-processed using df_explicit_na() explicit_na().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1:6)),   ANRIND = factor(c(rep(\"LOW\", 4), \"NORMAL\", \"HIGH\")),   BNRIND = factor(c(\"LOW\", \"NORMAL\", \"HIGH\", NA, \"LOW\", \"NORMAL\")) ) df <- df_explicit_na(df)  # Layout creating function. basic_table() %>%   count_abnormal_by_baseline(var = \"ANRIND\", abnormal = c(High = \"HIGH\")) %>%   build_table(df) #>                all obs   #> ———————————————————————— #> High                     #>   Not high    1/4 (25%)  #>   High           0/1     #>   Total      1/6 (16.7%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 2, 3, 4)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BLRANGE = factor(c(\"LOW\", \"HIGH\", \"HIGH\", \"NORMAL\")) )  basic_table() %>%   count_abnormal_by_baseline(     var = \"RANGE\",     abnormal = c(Low = \"LOW\"),     variables = list(id = \"ID\", baseline = \"BLRANGE\"),     .formats = c(fraction = \"xx / xx\"),     .indent_mods = c(fraction = 2L)   ) %>%   build_table(df2) #>                 all obs #> ——————————————————————— #> Low                     #>       Not low    1 / 3  #>       Low        0 / 1  #>       Total      1 / 4"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with marked laboratory abnormalities — abnormal_by_marked","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"analyze function count_abnormal_by_marked() creates layout element count patients marked laboratory abnormalities direction abnormality, categorized parameter value. function analyzes primary analysis variable var indicates whether single, replicated, last marked laboratory abnormality observed. Levels var include marked lab abnormality (single last_replicated) can supplied via category parameter. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, direction (defaults abn_dir), variable indicate abnormality directions. combination param direction levels, marked lab abnormality counts calculated follows: Single, last & Last replicated: number patients Single, last Last replicated values, respectively. : number patients either single replicated marked abnormalities. Fractions calculated dividing counts number patients least one valid measurement recorded analysis. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable direction.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"count_abnormal_by_marked(   lyt,   var,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )  a_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"lyt (PreDataTableLayouts) layout analyses added . category (list) list different marked category names single last replicated. variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Run get_stats(\"abnormal_by_marked\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_marked() table layout. s_count_abnormal_by_marked() returns statistic count_fraction Single, last, Last replicated, results. a_count_abnormal_by_marked() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_marked(): Statistics function patients marked lab abnormalities. a_count_abnormal_by_marked(): Formatted analysis function used afun count_abnormal_by_marked().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"Single, last Last replicated levels mutually exclusive. patient abnormalities meet Single, last Last replicated criteria, patient counted Last replicated category.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_marked.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(rep(1, 5), rep(2, 5), rep(1, 5), rep(2, 5))),   ARMCD = factor(c(rep(\"ARM A\", 5), rep(\"ARM B\", 5), rep(\"ARM A\", 5), rep(\"ARM B\", 5))),   ANRIND = factor(c(     \"NORMAL\", \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"HIGH\",     \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"NORMAL\", \"HIGH HIGH\", \"NORMAL\", \"LOW\", \"LOW\", \"LOW LOW\", \"LOW\",     \"LOW\", \"LOW\", \"LOW LOW\", \"NORMAL\", \"LOW LOW\"   )),   ONTRTFL = rep(c(\"\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\"), 2),   PARAMCD = factor(c(rep(\"CRP\", 10), rep(\"ALT\", 10))),   AVALCAT1 = factor(rep(c(\"\", \"\", \"\", \"SINGLE\", \"REPLICATED\", \"\", \"\", \"LAST\", \"\", \"SINGLE\"), 2)),   stringsAsFactors = FALSE )  df <- df %>%   mutate(abn_dir = factor(     case_when(       ANRIND == \"LOW LOW\" ~ \"Low\",       ANRIND == \"HIGH HIGH\" ~ \"High\",       TRUE ~ \"\"     ),     levels = c(\"Low\", \"High\")   ))  # Select only post-baseline records. df <- df %>% filter(ONTRTFL == \"Y\") df_crp <- df %>%   filter(PARAMCD == \"CRP\") %>%   droplevels() full_parent_df <- list(df_crp, \"not_needed\") cur_col_subset <- list(rep(TRUE, nrow(df_crp)), \"not_needed\") spl_context <- data.frame(   split = c(\"PARAMCD\", \"GRADE_DIR\"),   full_parent_df = I(full_parent_df),   cur_col_subset = I(cur_col_subset) )  map <- unique(   df[df$abn_dir %in% c(\"Low\", \"High\") & df$AVALCAT1 != \"\", c(\"PARAMCD\", \"abn_dir\")] ) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAMCD, abn_dir)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_to_map(map)   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_in_group(\"abn_dir\")   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"analyze function count_abnormal_by_worst_grade() creates layout element count patients highest (worst) analysis toxicity grade post-baseline direction, categorized parameter value. function analyzes primary analysis variable var indicates toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, grade_dir (defaults GRADE_DIR), variable indicate directions (e.g. High Low) toxicity grade supplied var. combination param grade_dir levels, patient counts worst grade calculated follows: 1 4: number patients worst grades 1-4, respectively. : number patients least one abnormality (.e. grade 0). Fractions calculated dividing counts number patients least one valid measurement recorded treatment. Pre-processing crucial using function can done automatically using h_adlb_abnormal_by_worst_grade() helper function. See description function details necessary pre-processing steps. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable grade_dir.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"count_abnormal_by_worst_grade(   lyt,   var,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )  a_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Run get_stats(\"abnormal_by_worst_grade\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_worst_grade() table layout. s_count_abnormal_by_worst_grade() returns single statistic count_fraction grades 1 4 \"\" results. a_count_abnormal_by_worst_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_worst_grade(): Statistics function counts patients worst grade. a_count_abnormal_by_worst_grade(): Formatted analysis function used afun count_abnormal_by_worst_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"library(dplyr) library(forcats) adlb <- tern_ex_adlb  # Data is modified in order to have some parameters with grades only in one direction # and simulate the real data. adlb$ATOXGR[adlb$PARAMCD == \"ALT\" & adlb$ATOXGR %in% c(\"1\", \"2\", \"3\", \"4\")] <- \"-1\" adlb$ANRIND[adlb$PARAMCD == \"ALT\" & adlb$ANRIND == \"HIGH\"] <- \"LOW\" adlb$WGRHIFL[adlb$PARAMCD == \"ALT\"] <- \"\"  adlb$ATOXGR[adlb$PARAMCD == \"IGA\" & adlb$ATOXGR %in% c(\"-1\", \"-2\", \"-3\", \"-4\")] <- \"1\" adlb$ANRIND[adlb$PARAMCD == \"IGA\" & adlb$ANRIND == \"LOW\"] <- \"HIGH\" adlb$WGRLOFL[adlb$PARAMCD == \"IGA\"] <- \"\"  # Pre-processing adlb_f <- adlb %>% h_adlb_abnormal_by_worst_grade()  # Map excludes records without abnormal grade since they should not be displayed # in the table. map <- unique(adlb_f[adlb_f$GRADE_DIR != \"ZERO\", c(\"PARAM\", \"GRADE_DIR\", \"GRADE_ANL\")]) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAM, desc(GRADE_DIR), GRADE_ANL)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAM\") %>%   split_rows_by(\"GRADE_DIR\", split_fun = trim_levels_to_map(map)) %>%   count_abnormal_by_worst_grade(     var = \"GRADE_ANL\",     variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\")   ) %>%   build_table(df = adlb_f) #>                                          ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————————————— #> Alanine Aminotransferase Measurement                                        #>   LOW                                                                       #>     1                                  12 (17.4%)    5 (6.8%)    8 (13.8%)  #>     2                                   9 (13%)     13 (17.8%)   6 (10.3%)  #>     3                                   6 (8.7%)     4 (5.5%)    6 (10.3%)  #>     4                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     Any                                34 (49.3%)   29 (39.7%)   26 (44.8%) #> C-Reactive Protein Measurement                                              #>   LOW                                                                       #>     1                                  11 (15.9%)   12 (16.4%)   7 (12.1%)  #>     2                                  8 (11.6%)     2 (2.7%)    6 (10.3%)  #>     3                                   4 (5.8%)    9 (12.3%)    6 (10.3%)  #>     4                                  7 (10.1%)     6 (8.2%)     4 (6.9%)  #>     Any                                30 (43.5%)   29 (39.7%)   23 (39.7%) #>   HIGH                                                                      #>     1                                  8 (11.6%)    11 (15.1%)    2 (3.4%)  #>     2                                   9 (13%)     11 (15.1%)    11 (19%)  #>     3                                  14 (20.3%)   10 (13.7%)    5 (8.6%)  #>     4                                   2 (2.9%)     4 (5.5%)    6 (10.3%)  #>     Any                                33 (47.8%)   36 (49.3%)   24 (41.4%) #> Immunoglobulin A Measurement                                                #>   HIGH                                                                      #>     1                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     2                                  8 (11.6%)     6 (8.2%)    8 (13.8%)  #>     3                                  7 (10.1%)     5 (6.8%)    9 (15.5%)  #>     4                                   6 (8.7%)     2 (2.7%)     3 (5.2%)  #>     Any                                28 (40.6%)   20 (27.4%)   26 (44.8%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"analyze function count_abnormal_lab_worsen_by_baseline() creates layout element count patients analysis toxicity grades worsened baseline, categorized highest (worst) grade post-baseline. function analyzes primary analysis variable var indicates analysis toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline_var (defaults BTOXGR), variable indicate baseline toxicity grades, direction_var (defaults GRADDIR), variable indicate toxicity grade directions interest include (e.g. \"H\" (high), \"L\" (low), \"B\" ()). direction(s) specified direction_var, patient counts worst grade patients worsened baseline calculated follows: 1 4: number patients worsened baseline grades worst grades 1-4, respectively. : total number patients worsened baseline grades. Fractions calculated dividing counts number patients analysis toxicity grades worsened baseline toxicity grades treatment. Prior using function table layout must use rtables::split_rows_by() create row split variable direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"count_abnormal_lab_worsen_by_baseline(   lyt,   var,   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )  a_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables including: id (string) subject variable name. baseline_var (string) name data column containing baseline toxicity variable. direction_var (string) see direction_var details. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"abnormal_by_worst_grade_worsen\") see available statistics. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_lab_worsen_by_baseline() table layout. s_count_abnormal_lab_worsen_by_baseline() returns counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\". a_count_abnormal_lab_worsen_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_lab_worsen_by_baseline(): Statistics function patients whose worst post-baseline lab grades worse baseline grades. a_count_abnormal_lab_worsen_by_baseline(): Formatted analysis function used afun count_abnormal_lab_worsen_by_baseline().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/abnormal_by_worst_grade_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   add_colcounts() %>%   split_rows_by(\"PARAMCD\") %>%   split_rows_by(\"GRADDR\") %>%   count_abnormal_lab_worsen_by_baseline(     var = \"ATOXGR\",     variables = list(       id = \"USUBJID\",       baseline_var = \"BTOXGR\",       direction_var = \"GRADDR\"     )   ) %>%   append_topleft(\"Direction of Abnormality\") %>%   build_table(df = df, alt_counts_df = tern_ex_adsl) #>                                ARM A           ARM B           ARM C     #> Direction of Abnormality      (N=69)          (N=73)          (N=58)     #> ———————————————————————————————————————————————————————————————————————— #> IGA                                                                      #>   High                                                                   #>     1                       6/63 (9.5%)     6/64 (9.4%)      4/50 (8%)   #>     2                      8/64 (12.5%)     5/67 (7.5%)    8/53 (15.1%)  #>     3                      7/66 (10.6%)     5/68 (7.4%)    9/57 (15.8%)  #>     4                       6/68 (8.8%)     2/72 (2.8%)     3/58 (5.2%)  #>     Any                    27/68 (39.7%)    18/72 (25%)    24/58 (41.4%) #> ALT                                                                      #>   High                                                                   #>     1                      7/63 (11.1%)     6/62 (9.7%)     2/48 (4.2%)  #>     2                       12/63 (19%)      4/67 (6%)      11/50 (22%)  #>     3                       4/65 (6.2%)    11/71 (15.5%)   7/56 (12.5%)  #>     4                       1/67 (1.5%)    8/71 (11.3%)      4/57 (7%)   #>     Any                    24/67 (35.8%)   29/71 (40.8%)   24/57 (42.1%) #>   Low                                                                    #>     1                      12/67 (17.9%)    4/66 (6.1%)    7/52 (13.5%)  #>     2                      9/68 (13.2%)    12/69 (17.4%)   6/55 (10.9%)  #>     3                       6/69 (8.7%)     4/71 (5.6%)     5/56 (8.9%)  #>     4                      7/69 (10.1%)     7/73 (9.6%)    6/58 (10.3%)  #>     Any                    34/69 (49.3%)    27/73 (37%)    24/58 (41.4%) #> CRP                                                                      #>   Low                                                                    #>     1                      11/66 (16.7%)   10/67 (14.9%)    4/47 (8.5%)  #>     2                      8/66 (12.1%)     1/70 (1.4%)     6/50 (12%)   #>     3                       4/68 (5.9%)    9/70 (12.9%)     5/53 (9.4%)  #>     4                      7/69 (10.1%)     6/72 (8.3%)     4/55 (7.3%)  #>     Any                    30/69 (43.5%)   26/72 (36.1%)   19/55 (34.5%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Split function to configure risk difference column — add_riskdiff","title":"Split function to configure risk difference column — add_riskdiff","text":"Wrapper function rtables::add_combo_levels() configures settings risk difference column added rtables object. add risk difference column table, function used split_fun calls rtables::split_cols_by(), followed setting argument riskdiff TRUE following analyze function calls.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"add_riskdiff(   arm_x,   arm_y,   col_label = paste0(\"Risk Difference (%) (95% CI)\", if (length(arm_y) > 1)     paste0(\"\\n\", arm_x, \" vs. \", arm_y)),   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split function to configure risk difference column — add_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split function to configure risk difference column — add_riskdiff","text":"closure suitable use split function (split_fun) within rtables::split_cols_by() creating table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/add_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"adae <- tern_ex_adae adae$AESEV <- factor(adae$AESEV)  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_riskdiff(arm_x = \"ARM A\", arm_y = c(\"ARM B\", \"ARM C\"))) %>%   count_occurrences_by_grade(     var = \"AESEV\",     riskdiff = TRUE   )  tbl <- build_table(lyt, df = adae) tbl #>                                                   Risk Difference (%) (95% CI)   Risk Difference (%) (95% CI) #>              ARM A        ARM B        ARM C            ARM A vs. ARM B                ARM A vs. ARM C        #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> MILD        6 (3.0%)     4 (2.3%)     2 (1.2%)          0.7 (-2.5 - 3.9)               1.7 (-1.2 - 4.6)       #> MODERATE   19 (9.4%)    15 (8.5%)    14 (8.6%)          0.9 (-4.8 - 6.7)               0.8 (-5.1 - 6.7)       #> SEVERE     34 (16.8%)   38 (21.5%)   32 (19.8%)        -4.6 (-12.6 - 3.3)             -2.9 (-10.9 - 5.1)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout-creating function to add row total counts — add_rowcounts","title":"Layout-creating function to add row total counts — add_rowcounts","text":"works analogously rtables::add_colcounts() rows. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"add_rowcounts(lyt, alt_counts = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout-creating function to add row total counts — add_rowcounts","text":"lyt (PreDataTableLayouts) layout analyses added . alt_counts (flag) whether row counts taken alt_counts_df (TRUE) df (FALSE). Defaults FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout-creating function to add row total counts — add_rowcounts","text":"modified layout latest row split labels now row-wise total counts (.e. without column-based subsetting) attached parentheses.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Layout-creating function to add row total counts — add_rowcounts","text":"Row count values contained row count rows displayed considered zero rows default pruning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/add_rowcounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"RACE\", split_fun = drop_split_levels) %>%   add_rowcounts() %>%   analyze(\"AGE\", afun = list_wrap_x(summary), format = \"xx.xx\") %>%   build_table(DM) #>                                    A: Drug X   B: Placebo   C: Combination #>                                     (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————————————————————————————————— #> ASIAN (N=231)                                                              #>   Min.                               20.00       21.00          22.00      #>   1st Qu.                            29.00       28.00          30.00      #>   Median                             33.00       32.50          33.50      #>   Mean                               34.20       32.68          34.63      #>   3rd Qu.                            38.50       36.00          38.00      #>   Max.                               58.00       55.00          53.00      #> BLACK OR AFRICAN AMERICAN (N=79)                                           #>   Min.                               23.00       21.00          24.00      #>   1st Qu.                            29.00       28.75          29.00      #>   Median                             33.00       30.00          32.00      #>   Mean                               34.68       31.71          34.00      #>   3rd Qu.                            37.25       36.25          39.00      #>   Max.                               60.00       42.00          51.00      #> WHITE (N=46)                                                               #>   Min.                               30.00       25.00          28.00      #>   1st Qu.                            38.00       31.00          30.25      #>   Median                             40.50       37.50          35.00      #>   Mean                               39.36       36.93          35.11      #>   3rd Qu.                            43.50       40.00          37.50      #>   Max.                               47.00       55.00          47.00"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for adverse event baskets — aesi_label","text":"","code":"aesi_label(aesi, scope = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for adverse event baskets — aesi_label","text":"aesi (character) vector standardized MedDRA query name (e.g. SMQxxNAM) customized query name (e.g. CQxxNAM). scope (character) vector scope query (e.g. SMQxxSC).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for adverse event baskets — aesi_label","text":"string standard label AE basket.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/aesi_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Labels for adverse event baskets — aesi_label","text":"","code":"adae <- tern_ex_adae  # Standardized query label includes scope. aesi_label(adae$SMQ01NAM, scope = adae$SMQ01SC) #> [1] \"C.1.1.1.3/B.2.2.3.1 aesi (BROAD)\"  # Customized query label. aesi_label(adae$CQ01NAM) #> [1] \"D.2.1.5.3/A.1.1.1.1 aesi\""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis function to calculate risk difference column values — afun_riskdiff","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"risk difference column, function uses statistics function associated afun calculates risk difference values arm X (reference group) arm Y. arms specified configuring risk difference column done using add_riskdiff() split function previous call rtables::split_cols_by(). columns, applies afun usual. function utilizes stat_propdiff_ci() function perform risk difference calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"","code":"afun_riskdiff(   df,   labelstr = \"\",   .var,   .N_col,   .N_row,   .df_row,   .spl_context,   .all_col_counts,   .stats,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   afun,   s_args = list() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .spl_context (data.frame) gives information ancestor split states passed rtables. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. afun (named list) named list containing one name-value pair name corresponds name statistics function used calculations value corresponding analysis function. s_args (named list) additional arguments passed statistics function analysis function supplied afun.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"list formatted rtables::CellValue().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Get selected statistics names — afun_selected_stats","title":"Get selected statistics names — afun_selected_stats","text":"Helper function used creating afun.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get selected statistics names — afun_selected_stats","text":"","code":"afun_selected_stats(.stats, all_stats)"},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get selected statistics names — afun_selected_stats","text":".stats (vector NULL) input layout creating function. Note NULL means context default statistics used. all_stats (character) statistics can selected potentially.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/afun_selected_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get selected statistics names — afun_selected_stats","text":"character vector selected statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_colvars_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions in columns — analyze_colvars_functions","title":"Analyze functions in columns — analyze_colvars_functions","text":"functions wrappers rtables::analyze_colvars() apply corresponding tern statistics functions add analysis given table layout. particular, functions designed analysis methods split different columns. analyze_vars_in_cols(): fundamental tabulation analysis methods onto columns. words, analysis methods defined column space, .e. become column labels. changing variable vector, list functions can applied different variables, caveat number statistical functions. tabulate_rsp_subgroups(): similarly analyze_vars_in_cols, function combines analyze_colvars summarize_row_groups compact way produce standard tables show analysis methods columns. tabulate_survival_subgroups(): function similar , used tables. analyze_patients_exposure_in_cols(): based analyze_colvars. needs summarize_patients_exposure_in_cols() leverage nesting label rows analysis rtables::summarize_row_groups(). summarize_coxreg(): generally based rtables::summarize_row_groups(), behaves similarly tabulate_* functions described designed provide specific standard tables may contain nested structure combination summarize_row_groups() rtables::analyze_colvars().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions — analyze_functions","title":"Analyze functions — analyze_functions","text":"functions wrappers rtables::analyze() apply corresponding tern statistics functions add analysis given table layout: analyze_num_patients() analyze_vars() compare_vars() count_abnormal() count_abnormal_by_baseline() count_abnormal_by_marked() count_abnormal_by_worst_grade() count_cumulative() count_missed_doses() count_occurrences() count_occurrences_by_grade() count_patients_events_in_cols() count_patients_with_event() count_patients_with_flags() count_values() coxph_pairwise() estimate_incidence_rate() estimate_multinomial_rsp() estimate_odds_ratio() estimate_proportion() estimate_proportion_diff() summarize_ancova() summarize_colvars(): even function uses rtables::analyze_colvars(), applies analysis methods different rows one variables split different columns. comparison, analyze_colvars_functions leverage analyze_colvars context split rows analysis methods columns. summarize_change() surv_time() surv_timepoint() test_proportion_diff()","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze variables — analyze_variables","title":"Analyze variables — analyze_variables","text":"analyze function analyze_vars() creates layout element summarize one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\") non-numeric variables running get_stats(\"analyze_vars_counts\"). Use .stats parameter specify statistics include output summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze variables — analyze_variables","text":"","code":"analyze_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)  # S3 method for class 'numeric' s_summary(   x,   na.rm = TRUE,   denom,   .N_row,   .N_col,   .var,   control = control_analyze_vars(),   ... )  # S3 method for class 'factor' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   ... )  # S3 method for class 'character' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   ... )  a_summary(   x,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .ref_group = NULL,   .in_ref_col = FALSE,   compare = FALSE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na.rm = TRUE,   na_str = default_na_str(),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze variables — analyze_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_summary(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Run get_stats(\"analyze_vars_numeric\") see statistics available numeric variables, get_stats(\"analyze_vars_counts\") statistics available non-numeric variables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .var (string) single variable name passed rtables requested statistics function. control (list) parameters descriptive statistics details, specified using helper function control_analyze_vars(). possible parameter options : conf_level (proportion) confidence level interval mean median. quantiles (numeric(2)) vector length two specify quantiles. quantile_type (numeric(1)) 1 9 selecting quantile algorithms used. See type stats::quantile(). test_mean (numeric(1)) value test mean null hypothesis calculating p-value. verbose (flag) defaults TRUE, prints warnings messages. mainly used print information factor casting. .df_row (data.frame) data frame across columns given row split. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. compare (flag) whether comparison statistics analyzed instead summary statistics (compare = TRUE adds pval statistic comparing reference group).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze variables — analyze_variables","text":"analyze_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_summary() table layout. s_summary() returns different statistics depending class x. x class numeric, returns list following named numeric items: n: length() x. sum: sum() x. mean: mean() x. sd: stats::sd() x. se: standard error x mean, .e.: (sd(x) / sqrt(length(x))). mean_sd: mean() stats::sd() x. mean_se: mean() x standard error (see ). mean_ci: CI mean x (stat_mean_ci()). mean_sei: SE interval mean x, .e.: (mean() -/+ stats::sd() / sqrt()). mean_sdi: SD interval mean x, .e.: (mean() -/+ stats::sd()). mean_pval: two-sided p-value mean x (stat_mean_pval()). median: stats::median() x. mad: median absolute deviation x, .e.: (stats::median() xc, xc = x - stats::median()). median_ci: CI median x (stat_median_ci()). quantiles: Two sample quantiles x (stats::quantile()). iqr: stats::IQR() x. range: range_noinf() x. min: max() x. max: min() x. median_range: median() range_noinf() x. cv: coefficient variation x, .e.: (stats::sd() / mean() * 100). geom_mean: geometric mean x, .e.: (exp(mean(log(x)))). geom_cv: geometric coefficient variation x, .e.: (sqrt(exp(sd(log(x)) ^ 2) - 1) * 100). x class factor converted character, returns list named numeric items: n: length() x. count: list number cases level factor x. count_fraction: Similar count also includes proportion cases level factor x relative denominator, NA denominator zero. x class logical, returns list named numeric items: n: length() x (possibly removing NAs). count: Count TRUE x. count_fraction: Count proportion TRUE x relative denominator, NA denominator zero. Note NAs x never counted leading NA . a_summary() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Analyze variables — analyze_variables","text":"Automatic digit formatting: number digits display can automatically determined analyzed variable(s) (vars) certain statistics setting statistic format \"auto\" .formats. utilizes format_auto() formatting function. Note data current row & variable (columns) considered (.df_row[[.var]], see rtables::additional_fun_params) whole dataset.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze variables — analyze_variables","text":"analyze_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_summary(): S3 generic function produces variable summary. s_summary(numeric): Method numeric class. s_summary(factor): Method factor class. s_summary(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_summary(logical): Method logical class. a_summary(): Formatted analysis function used afun analyze_vars() compare_vars() cfun summarize_colvars().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze variables — analyze_variables","text":"x empty vector, NA returned. expected feature return rcell content rtables intersection column row delimits empty data selection. mean function applied empty vector, NA returned instead NaN, latter standard behavior R. x empty factor, list still returned counts one element per factor level. levels x, function fails. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. Automatic conversion character factor guarantee table can generated correctly. particular sparse tables likely can fail. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table(). use comparison (additional p-value statistic), parameter compare must set TRUE. Ensure either NA values converted explicit NA level NA values left .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze variables — analyze_variables","text":"","code":"## Fabricated dataset. dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVAL    = c(9:1, rep(NA, 9)) )  # `analyze_vars()` in `rtables` pipelines ## Default output within a `rtables` pipeline. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  build_table(l, df = dta_test) #>                   A           B       C  #> ———————————————————————————————————————— #> V1                                       #>   n               2           1       0  #>   Mean (SD)   7.5 (2.1)   3.0 (NA)    NA #>   Median         7.5         3.0      NA #>   Min - Max   6.0 - 9.0   3.0 - 3.0   NA #> V2                                       #>   n               2           1       0  #>   Mean (SD)   6.5 (2.1)   2.0 (NA)    NA #>   Median         6.5         2.0      NA #>   Min - Max   5.0 - 8.0   2.0 - 2.0   NA #> V3                                       #>   n               2           1       0  #>   Mean (SD)   5.5 (2.1)   1.0 (NA)    NA #>   Median         5.5         1.0      NA #>   Min - Max   4.0 - 7.0   1.0 - 1.0   NA  ## Select and format statistics output. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(     vars = \"AVAL\",     .stats = c(\"n\", \"mean_sd\", \"quantiles\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\", quantiles = c(\"Q1 - Q3\"))   )  build_table(l, df = dta_test) #>                  A           B       C  #> ——————————————————————————————————————— #> V1                                      #>   n              2           1       0  #>   Mean, SD   7.5, 2.1     3.0, NA    NA #>   Q1 - Q3    6.0 - 9.0   3.0 - 3.0   NA #> V2                                      #>   n              2           1       0  #>   Mean, SD   6.5, 2.1     2.0, NA    NA #>   Q1 - Q3    5.0 - 8.0   2.0 - 2.0   NA #> V3                                      #>   n              2           1       0  #>   Mean, SD   5.5, 2.1     1.0, NA    NA #>   Q1 - Q3    4.0 - 7.0   1.0 - 1.0   NA  ## Use arguments interpreted by `s_summary`. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", na.rm = FALSE)  build_table(l, df = dta_test) #>                   A       B    C  #> ————————————————————————————————— #> V1                                #>   n               2       2    2  #>   Mean (SD)   7.5 (2.1)   NA   NA #>   Median         7.5      NA   NA #>   Min - Max   6.0 - 9.0   NA   NA #> V2                                #>   n               2       2    2  #>   Mean (SD)   6.5 (2.1)   NA   NA #>   Median         6.5      NA   NA #>   Min - Max   5.0 - 8.0   NA   NA #> V3                                #>   n               2       2    2  #>   Mean (SD)   5.5 (2.1)   NA   NA #>   Median         5.5      NA   NA #>   Min - Max   4.0 - 7.0   NA   NA  ## Handle `NA` levels first when summarizing factors. dta_test$AVISIT <- NA_character_ dta_test <- df_explicit_na(dta_test) l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   analyze_vars(vars = \"AVISIT\", na.rm = FALSE)  build_table(l, df = dta_test) #>                A          B          C     #> —————————————————————————————————————————— #> n              6          6          6     #> <Missing>   6 (100%)   6 (100%)   6 (100%)  # auto format dt <- data.frame(\"VAR\" = c(0.001, 0.2, 0.0011000, 3, 4)) basic_table() %>%   analyze_vars(     vars = \"VAR\",     .stats = c(\"n\", \"mean\", \"mean_sd\", \"range\"),     .formats = c(\"mean_sd\" = \"auto\", \"range\" = \"auto\")   ) %>%   build_table(dt) #>                  all obs      #> ————————————————————————————— #> n                   5         #> Mean               1.4        #> Mean (SD)   1.44042 (1.91481) #> Min - Max    0.0010 - 4.0000   # `s_summary.numeric`  ## Basic usage: empty numeric returns NA-filled items. s_summary(numeric()) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>   ## Management of NA values. x <- c(NA_real_, 1) s_summary(x, na.rm = TRUE) #> $n #> n  #> 1  #>  #> $sum #> sum  #>   1  #>  #> $mean #> mean  #>    1  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>    1   NA  #>  #> $mean_se #> mean   se  #>    1   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>      1  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             1  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   0  #>  #> $range #> min max  #>   1   1  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   1  #>  #> $median_range #> median    min    max  #>      1      1      1  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>         1  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  s_summary(x, na.rm = FALSE) #> $n #> n  #> 2  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>        NA  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>   x <- c(NA_real_, 1, 2) s_summary(x, stats = NULL) #> $n #> n  #> 2  #>  #> $sum #> sum  #>   3  #>  #> $mean #> mean  #>  1.5  #>  #> $sd #>        sd  #> 0.7071068  #>  #> $se #>  se  #> 0.5  #>  #> $mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $mean_se #> mean   se  #>  1.5  0.5  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>    1.5  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   1  #>  #> $range #> min max  #>   1   2  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   2  #>  #> $median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 47.14045  #>  #> $geom_mean #> geom_mean  #>  1.414214  #>  #> $geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 52.10922  #>   ## Benefits in `rtables` contructions: dta_test <- data.frame(   Group = rep(LETTERS[1:3], each = 2),   sub_group = rep(letters[1:2], each = 3),   x = 1:6 )  ## The summary obtained in with `rtables`: basic_table() %>%   split_cols_by(var = \"Group\") %>%   split_rows_by(var = \"sub_group\") %>%   analyze(vars = \"x\", afun = s_summary) %>%   build_table(df = dta_test) #>                                                  A                        B                       C                   #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> a                                                                                                                     #>   n                                              2                        1                       0                   #>   sum                                            3                        3                       NA                  #>   mean                                          1.5                       3                       NA                  #>   sd                                     0.707106781186548               NA                       NA                  #>   se                                            0.5                      NA                       NA                  #>   mean_sd                              1.5, 0.707106781186548           3, NA                     NA                  #>   mean_se                                     1.5, 0.5                  3, NA                     NA                  #>   Mean 95% CI                   -4.85310236808735, 7.85310236808735      NA                       NA                  #>   Mean -/+ 1xSE                                 1, 2                     NA                       NA                  #>   Mean -/+ 1xSD                 0.792893218813452, 2.20710678118655      NA                       NA                  #>   Mean p-value (H0: mean = 0)            0.204832764699133               NA                       NA                  #>   median                                        1.5                       3                       NA                  #>   mad                                            0                        0                       NA                  #>   Median 95% CI                                  NA                      NA                       NA                  #>   25% and 75%-ile                               1, 2                    3, 3                      NA                  #>   iqr                                            1                        0                       NA                  #>   range                                         1, 2                    3, 3                      NA                  #>   min                                            1                        3                       NA                  #>   max                                            2                        3                       NA                  #>   Median (Min - Max)                         1.5, 1, 2                 3, 3, 3                    NA                  #>   cv                                      47.1404520791032               NA                       NA                  #>   geom_mean                               1.41421356237309                3                       NA                  #>   Geometric Mean 95% CI         0.0172997815631007, 115.608396135236     NA                       NA                  #>   geom_cv                                 52.1092246837487               NA                       NA                  #> b                                                                                                                     #>   n                                              0                        1                       2                   #>   sum                                            NA                       4                       11                  #>   mean                                           NA                       4                      5.5                  #>   sd                                             NA                      NA               0.707106781186548           #>   se                                             NA                      NA                      0.5                  #>   mean_sd                                        NA                     4, NA           5.5, 0.707106781186548        #>   mean_se                                        NA                     4, NA                  5.5, 0.5               #>   Mean 95% CI                                    NA                      NA      -0.853102368087347, 11.8531023680873 #>   Mean -/+ 1xSE                                  NA                      NA                      5, 6                 #>   Mean -/+ 1xSD                                  NA                      NA       4.79289321881345, 6.20710678118655  #>   Mean p-value (H0: mean = 0)                    NA                      NA               0.0577158767526089          #>   median                                         NA                       4                      5.5                  #>   mad                                            NA                       0                       0                   #>   Median 95% CI                                  NA                      NA                       NA                  #>   25% and 75%-ile                                NA                     4, 4                     5, 6                 #>   iqr                                            NA                       0                       1                   #>   range                                          NA                     4, 4                     5, 6                 #>   min                                            NA                       4                       5                   #>   max                                            NA                       4                       6                   #>   Median (Min - Max)                             NA                    4, 4, 4                5.5, 5, 6               #>   cv                                             NA                      NA                12.8564869306645           #>   geom_mean                                      NA                       4                5.47722557505166           #>   Geometric Mean 95% CI                          NA                      NA       1.71994304449266, 17.4424380482025  #>   geom_cv                                        NA                      NA                12.945835316564             ## By comparison with `lapply`: X <- split(dta_test, f = with(dta_test, interaction(Group, sub_group))) lapply(X, function(x) s_summary(x$x)) #> $A.a #> $A.a$n #> n  #> 2  #>  #> $A.a$sum #> sum  #>   3  #>  #> $A.a$mean #> mean  #>  1.5  #>  #> $A.a$sd #>        sd  #> 0.7071068  #>  #> $A.a$se #>  se  #> 0.5  #>  #> $A.a$mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $A.a$mean_se #> mean   se  #>  1.5  0.5  #>  #> $A.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.a$mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.a$median #> median  #>    1.5  #>  #> $A.a$mad #> mad  #>   0  #>  #> $A.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.a$quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.a$iqr #> iqr  #>   1  #>  #> $A.a$range #> min max  #>   1   2  #>  #> $A.a$min #> min  #>   1  #>  #> $A.a$max #> max  #>   2  #>  #> $A.a$median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.a$cv #>       cv  #> 47.14045  #>  #> $A.a$geom_mean #> geom_mean  #>  1.414214  #>  #> $A.a$geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.a$geom_cv #>  geom_cv  #> 52.10922  #>  #>  #> $B.a #> $B.a$n #> n  #> 1  #>  #> $B.a$sum #> sum  #>   3  #>  #> $B.a$mean #> mean  #>    3  #>  #> $B.a$sd #> sd  #> NA  #>  #> $B.a$se #> se  #> NA  #>  #> $B.a$mean_sd #> mean   sd  #>    3   NA  #>  #> $B.a$mean_se #> mean   se  #>    3   NA  #>  #> $B.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.a$median #> median  #>      3  #>  #> $B.a$mad #> mad  #>   0  #>  #> $B.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.a$quantiles #> quantile_0.25 quantile_0.75  #>             3             3  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.a$iqr #> iqr  #>   0  #>  #> $B.a$range #> min max  #>   3   3  #>  #> $B.a$min #> min  #>   3  #>  #> $B.a$max #> max  #>   3  #>  #> $B.a$median_range #> median    min    max  #>      3      3      3  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.a$cv #> cv  #> NA  #>  #> $B.a$geom_mean #> geom_mean  #>         3  #>  #> $B.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.a$geom_cv #> geom_cv  #>      NA  #>  #>  #> $C.a #> $C.a$n #> n  #> 0  #>  #> $C.a$sum #> sum  #>  NA  #>  #> $C.a$mean #> mean  #>   NA  #>  #> $C.a$sd #> sd  #> NA  #>  #> $C.a$se #> se  #> NA  #>  #> $C.a$mean_sd #> mean   sd  #>   NA   NA  #>  #> $C.a$mean_se #> mean   se  #>   NA   NA  #>  #> $C.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.a$median #> median  #>     NA  #>  #> $C.a$mad #> mad  #>  NA  #>  #> $C.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.a$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.a$iqr #> iqr  #>  NA  #>  #> $C.a$range #> min max  #>  NA  NA  #>  #> $C.a$min #> min  #>  NA  #>  #> $C.a$max #> max  #>  NA  #>  #> $C.a$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.a$cv #> cv  #> NA  #>  #> $C.a$geom_mean #> geom_mean  #>       NaN  #>  #> $C.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.a$geom_cv #> geom_cv  #>      NA  #>  #>  #> $A.b #> $A.b$n #> n  #> 0  #>  #> $A.b$sum #> sum  #>  NA  #>  #> $A.b$mean #> mean  #>   NA  #>  #> $A.b$sd #> sd  #> NA  #>  #> $A.b$se #> se  #> NA  #>  #> $A.b$mean_sd #> mean   sd  #>   NA   NA  #>  #> $A.b$mean_se #> mean   se  #>   NA   NA  #>  #> $A.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.b$median #> median  #>     NA  #>  #> $A.b$mad #> mad  #>  NA  #>  #> $A.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.b$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.b$iqr #> iqr  #>  NA  #>  #> $A.b$range #> min max  #>  NA  NA  #>  #> $A.b$min #> min  #>  NA  #>  #> $A.b$max #> max  #>  NA  #>  #> $A.b$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.b$cv #> cv  #> NA  #>  #> $A.b$geom_mean #> geom_mean  #>       NaN  #>  #> $A.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.b$geom_cv #> geom_cv  #>      NA  #>  #>  #> $B.b #> $B.b$n #> n  #> 1  #>  #> $B.b$sum #> sum  #>   4  #>  #> $B.b$mean #> mean  #>    4  #>  #> $B.b$sd #> sd  #> NA  #>  #> $B.b$se #> se  #> NA  #>  #> $B.b$mean_sd #> mean   sd  #>    4   NA  #>  #> $B.b$mean_se #> mean   se  #>    4   NA  #>  #> $B.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.b$median #> median  #>      4  #>  #> $B.b$mad #> mad  #>   0  #>  #> $B.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.b$quantiles #> quantile_0.25 quantile_0.75  #>             4             4  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.b$iqr #> iqr  #>   0  #>  #> $B.b$range #> min max  #>   4   4  #>  #> $B.b$min #> min  #>   4  #>  #> $B.b$max #> max  #>   4  #>  #> $B.b$median_range #> median    min    max  #>      4      4      4  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.b$cv #> cv  #> NA  #>  #> $B.b$geom_mean #> geom_mean  #>         4  #>  #> $B.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.b$geom_cv #> geom_cv  #>      NA  #>  #>  #> $C.b #> $C.b$n #> n  #> 2  #>  #> $C.b$sum #> sum  #>  11  #>  #> $C.b$mean #> mean  #>  5.5  #>  #> $C.b$sd #>        sd  #> 0.7071068  #>  #> $C.b$se #>  se  #> 0.5  #>  #> $C.b$mean_sd #>      mean        sd  #> 5.5000000 0.7071068  #>  #> $C.b$mean_se #> mean   se  #>  5.5  0.5  #>  #> $C.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>            5            6  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     4.792893     6.207107  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.b$mean_pval #>    p_value  #> 0.05771588  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.b$median #> median  #>    5.5  #>  #> $C.b$mad #> mad  #>   0  #>  #> $C.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.b$quantiles #> quantile_0.25 quantile_0.75  #>             5             6  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.b$iqr #> iqr  #>   1  #>  #> $C.b$range #> min max  #>   5   6  #>  #> $C.b$min #> min  #>   5  #>  #> $C.b$max #> max  #>   6  #>  #> $C.b$median_range #> median    min    max  #>    5.5    5.0    6.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.b$cv #>       cv  #> 12.85649  #>  #> $C.b$geom_mean #> geom_mean  #>  5.477226  #>  #> $C.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.b$geom_cv #>  geom_cv  #> 12.94584  #>  #>   # `s_summary.factor`  ## Basic usage: s_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\"))) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(factor(levels = c(\"a\", \"b\", \"c\"))) #> $n #> [1] 0 #>  #> $count #> $count$a #> [1] 0 #>  #> $count$b #> [1] 0 #>  #> $count$c #> [1] 0 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 0 0 #>  #> $count_fraction$b #> [1] 0 0 #>  #> $count_fraction$c #> [1] 0 0 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     0     0  #>  #> $fraction$b #>   num denom  #>     0     0  #>  #> $fraction$c #>   num denom  #>     0     0  #>  #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- factor(c(NA, \"Female\")) x <- explicit_na(x) s_summary(x, na.rm = TRUE) #> $n #> [1] 1 #>  #> $count #> $count$Female #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1 1 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     1  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 2 #>  #> $count #> $count$Female #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1.0 0.5 #>  #> $count_fraction$`<Missing>` #> [1] 1.0 0.5 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     2  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     2  #>  #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.3 #>  #> $count_fraction$b #> [1] 1.0 0.1 #>  #> $count_fraction$c #> [1] 1.0 0.1 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    10  #>  #> $fraction$b #>   num denom  #>     1    10  #>  #> $fraction$c #>   num denom  #>     1    10  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.00 0.15 #>  #> $count_fraction$b #> [1] 1.00 0.05 #>  #> $count_fraction$c #> [1] 1.00 0.05 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    20  #>  #> $fraction$b #>   num denom  #>     1    20  #>  #> $fraction$c #>   num denom  #>     1    20  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.character`  ## Basic usage: s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\"), .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\", \"\"), .var = \"x\", na.rm = FALSE, verbose = FALSE) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`NA` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`NA` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`NA` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.logical`  ## Basic usage: s_summary(c(TRUE, FALSE, TRUE, TRUE)) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(as.logical(c())) #> $n #> [1] 0 #>  #> $count #> [1] 0 #>  #> $count_fraction #> [1] 0 0 #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) s_summary(x, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- c(TRUE, FALSE, TRUE, TRUE) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.0 0.3 #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.15 #>  #> $n_blq #> [1] 0 #>   a_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              5          0         n #> 2                    count.a              3          0         a #> 3                    count.b              1          0         b #> 4                    count.c              1          0         c #> 5           count_fraction.a        3 (60%)          0         a #> 6           count_fraction.b        1 (20%)          0         b #> 7           count_fraction.c        1 (20%)          0         c #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0         a #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0         b #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0         c #> 11                fraction.a    3/5 (60.0%)          0         a #> 12                fraction.b    1/5 (20.0%)          0         b #> 13                fraction.c    1/5 (20.0%)          0         c #> 14                     n_blq              0          0     n_blq a_summary(   factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")),   .ref_group = factor(c(\"a\", \"a\", \"b\", \"c\")), compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              5          0 #> 2                    count.a              3          0 #> 3                    count.b              1          0 #> 4                    count.c              1          0 #> 5           count_fraction.a        3 (60%)          0 #> 6           count_fraction.b        1 (20%)          0 #> 7           count_fraction.c        1 (20%)          0 #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0 #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0 #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0 #> 11                fraction.a    3/5 (60.0%)          0 #> 12                fraction.b    1/5 (20.0%)          0 #> 13                fraction.c    1/5 (20.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9560          0 #>                     row_label #> 1                           n #> 2                           a #> 3                           b #> 4                           c #> 5                           a #> 6                           b #> 7                           c #> 8                           a #> 9                           b #> 10                          c #> 11                          a #> 12                          b #> 13                          c #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(\"A\", \"B\", \"A\", \"C\"), .var = \"x\", .N_col = 10, .N_row = 10, verbose = FALSE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              4          0         n #> 2                    count.A              2          0         A #> 3                    count.B              1          0         B #> 4                    count.C              1          0         C #> 5           count_fraction.A        2 (50%)          0         A #> 6           count_fraction.B        1 (25%)          0         B #> 7           count_fraction.C        1 (25%)          0         C #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0         A #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0         B #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0         C #> 11                fraction.A    2/4 (50.0%)          0         A #> 12                fraction.B    1/4 (25.0%)          0         B #> 13                fraction.C    1/4 (25.0%)          0         C #> 14                     n_blq              0          0     n_blq a_summary(   c(\"A\", \"B\", \"A\", \"C\"),   .ref_group = c(\"B\", \"A\", \"C\"), .var = \"x\", compare = TRUE, verbose = FALSE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              4          0 #> 2                    count.A              2          0 #> 3                    count.B              1          0 #> 4                    count.C              1          0 #> 5           count_fraction.A        2 (50%)          0 #> 6           count_fraction.B        1 (25%)          0 #> 7           count_fraction.C        1 (25%)          0 #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0 #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0 #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0 #> 11                fraction.A    2/4 (50.0%)          0 #> 12                fraction.B    1/4 (25.0%)          0 #> 13                fraction.C    1/4 (25.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9074          0 #>                     row_label #> 1                           n #> 2                           A #> 3                           B #> 4                           C #> 5                           A #> 6                           B #> 7                           C #> 8                           A #> 9                           B #> 10                          C #> 11                          A #> 12                          B #> 13                          C #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(TRUE, FALSE, FALSE, TRUE, TRUE), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n              5          0              n #> 2                   count              3          0          count #> 3          count_fraction        3 (60%)          0 count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0 count_fraction #> 5                fraction                         0       fraction #> 6                   n_blq              0          0          n_blq a_summary(   c(TRUE, FALSE, FALSE, TRUE, TRUE),   .ref_group = c(TRUE, FALSE), .in_ref_col = TRUE, compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod                  row_label #> 1                       n              5          0                          n #> 2                   count              3          0                      count #> 3          count_fraction        3 (60%)          0             count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0             count_fraction #> 5                fraction                         0                   fraction #> 6                   n_blq              0          0                      n_blq #> 7             pval_counts                         0 p-value (chi-squared test)  a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = \"bla\") #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>        row_name    formatted_cell indent_mod                   row_label #> 1             n                10          0                           n #> 2           sum              -4.4          0                         Sum #> 3          mean              -0.4          0                        Mean #> 4            sd               1.1          0                          SD #> 5            se               0.4          0                          SE #> 6       mean_sd        -0.4 (1.1)          0                   Mean (SD) #> 7       mean_se        -0.4 (0.4)          0                   Mean (SE) #> 8       mean_ci     (-1.24, 0.36)          0                 Mean 95% CI #> 9      mean_sei    (-0.79, -0.09)          0               Mean -/+ 1xSE #> 10     mean_sdi     (-1.56, 0.68)          0               Mean -/+ 1xSD #> 11    mean_pval            0.2432          0 Mean p-value (H0: mean = 0) #> 12       median              -0.2          0                      Median #> 13          mad               0.0          0   Median Absolute Deviation #> 14    median_ci     (-1.82, 0.62)          0               Median 95% CI #> 15    quantiles        -1.4 - 0.3          0             25% and 75%-ile #> 16          iqr               1.7          0                         IQR #> 17        range        -2.4 - 1.1          0                   Min - Max #> 18          min              -2.4          0                     Minimum #> 19          max               1.1          0                     Maximum #> 20 median_range -0.2 (-2.4 - 1.1)          0          Median (Min - Max) #> 21           cv            -253.2          0                      CV (%) #> 22    geom_mean                NA          0              Geometric Mean #> 23 geom_mean_ci                NA          0       Geometric Mean 95% CI #> 24      geom_cv                NA          0         CV % Geometric Mean a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = \"bla\", compare = TRUE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>        row_name  formatted_cell indent_mod                   row_label #> 1             n              10          0                           n #> 2           sum            48.2          0                         Sum #> 3          mean             4.8          0                        Mean #> 4            sd             1.2          0                          SD #> 5            se             0.4          0                          SE #> 6       mean_sd       4.8 (1.2)          0                   Mean (SD) #> 7       mean_se       4.8 (0.4)          0                   Mean (SE) #> 8       mean_ci    (3.98, 5.66)          0                 Mean 95% CI #> 9      mean_sei    (4.45, 5.19)          0               Mean -/+ 1xSE #> 10     mean_sdi    (3.65, 6.00)          0               Mean -/+ 1xSD #> 11    mean_pval         <0.0001          0 Mean p-value (H0: mean = 0) #> 12       median             4.7          0                      Median #> 13          mad             0.0          0   Median Absolute Deviation #> 14    median_ci    (3.37, 5.63)          0               Median 95% CI #> 15    quantiles       4.1 - 5.5          0             25% and 75%-ile #> 16          iqr             1.5          0                         IQR #> 17        range       3.1 - 7.1          0                   Min - Max #> 18          min             3.1          0                     Minimum #> 19          max             7.1          0                     Maximum #> 20 median_range 4.7 (3.1 - 7.1)          0          Median (Min - Max) #> 21           cv            24.4          0                      CV (%) #> 22    geom_mean             4.7          0              Geometric Mean #> 23 geom_mean_ci    (3.93, 5.60)          0       Geometric Mean 95% CI #> 24      geom_cv            25.2          0         CV % Geometric Mean #> 25         pval         <0.0001          0            p-value (t-test)"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze numeric variables in columns — analyze_vars_in_cols","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout-creating function analyze_vars_in_cols() creates layout element generate column-wise analysis table. function sets analysis methods column labels wrapper rtables::analyze_colvars(). designed principally PK tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"analyze_vars_in_cols(   lyt,   vars,   ...,   .stats = c(\"n\", \"mean\", \"sd\", \"se\", \"cv\", \"geom_cv\"),   .labels = c(n = \"n\", mean = \"Mean\", sd = \"SD\", se = \"SE\", cv = \"CV (%)\", geom_cv =     \"CV % Geometric Mean\"),   row_labels = NULL,   do_summarize_row_groups = FALSE,   split_col_vars = TRUE,   imp_rule = NULL,   avalcat_var = \"AVALCAT1\",   cache = FALSE,   .indent_mods = NULL,   na_str = default_na_str(),   nested = TRUE,   .formats = NULL,   .aligns = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . ... additional arguments lower level functions. .stats (character) statistics select table. .labels (named character) labels statistics (without indent). row_labels (character) function works columns space, usually .labels character vector applies column space. can change row labels defining parameter named character vector names corresponding split values. defaults NULL contains one string, duplicate row label. do_summarize_row_groups (flag) defaults FALSE applies analysis current label rows. wrapper rtables::summarize_row_groups() can accept labelstr define row labels. behavior supported never need overload row labels. split_col_vars (flag) defaults TRUE puts analysis results onto columns. option allows add multiple instances functions, also nested fashion, without adding splits. split must happen one time single layout. imp_rule (string NULL) imputation rule setting. Defaults NULL imputation rule. Can also \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. order use imputation rule, avalcat_var argument must specified. See imputation_rule() details imputation. avalcat_var (string) imp_rule NULL, name variable indicates whether row data corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable must present data match variable used calculate n_blq statistic (included .stats). cache (flag) whether store computed values temporary caching environment. speed calculations large tables, set FALSE rtable layout used multiple tables different data. Defaults FALSE. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"experimental implementation rtables::summarize_row_groups() rtables::analyze_colvars() may subjected changes rtables extends support complex analysis pipelines column space. encourage users read examples carefully file issues different use cases. function, labelstr behaves atypically. labelstr = NULL (default), row labels assigned automatically split values do_summarize_row_groups = FALSE (default), group label do_summarize_row_groups = TRUE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/analyze_vars_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"library(dplyr)  # Data preparation adpp <- tern_ex_adpp %>% h_pkparam_sort()  lyt <- basic_table() %>%   split_rows_by(var = \"STRATA1\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>% # Removes duplicated labels   analyze_vars_in_cols(vars = \"AGE\") result <- build_table(lyt = lyt, df = adpp) result #> STRATA1                                                          #>   SEX      n    Mean    SD    SE    CV (%)   CV % Geometric Mean #> ———————————————————————————————————————————————————————————————— #> A                                                                #>   F       81    38.8   5.4    0.6    13.8           14.3         #>   M       81    38.9   5.9    0.7    15.1           14.9         #> B                                                                #>   F       90    36.0   6.4    0.7    17.7           17.9         #>   M       81    36.4   6.5    0.7    17.9           17.8         #> C                                                                #>   F       117   34.1   6.2    0.6    18.2           18.3         #>   M       72    33.2   11.5   1.4    34.6           31.6          # By selecting just some statistics and ad-hoc labels lyt <- basic_table() %>%   split_rows_by(var = \"ARM\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\",     split_fun = drop_split_levels   ) %>%   analyze_vars_in_cols(     vars = \"AGE\",     .stats = c(\"n\", \"cv\", \"geom_mean\"),     .labels = c(       n = \"aN\",       cv = \"aCV\",       geom_mean = \"aGeomMean\"     )   ) result <- build_table(lyt = lyt, df = adpp) result #> ARM                                     #>   SEX            aN    aCV    aGeomMean #> ——————————————————————————————————————— #> A: Drug X                               #> B: Placebo                              #> C: Combination                          #>   F              288   17.6     35.5    #>   M              234   23.4     35.3     # Changing row labels lyt <- basic_table() %>%   analyze_vars_in_cols(     vars = \"AGE\",     row_labels = \"some custom label\"   ) result <- build_table(lyt, df = adpp) result #>                      n    Mean   SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————————— #> some custom label   522   36.1   7.4   0.3    20.4           20.6          # Pharmacokinetic parameters lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\"   ) result <- build_table(lyt, df = adpp) result #> PK Parameter   n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4          # Multiple calls (summarize label and analyze underneath) lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     do_summarize_row_groups = TRUE # does a summarize level   ) %>%   split_rows_by(\"SEX\",     child_labels = \"hidden\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     split_col_vars = FALSE # avoids re-splitting the columns   ) result <- build_table(lyt, df = adpp) result #> PK Parameter                                                          #>   SEX          n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #>   F            32   30.1    6.1    1.1    20.4           21.0         #>   M            26   29.2    5.0    1.0    17.2           17.2         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #>   F            32   209.5   43.3   7.7    20.7           21.6         #>   M            26   205.0   20.9   4.1    10.2           10.4         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #>   F            32    5.1    1.1    0.2    20.8           23.2         #>   M            26    5.1    1.1    0.2    20.7           22.5         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #>   F            32    1.5    0.3    0.1    19.3           20.8         #>   M            26    1.5    0.4    0.1    23.9           27.9         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #>   F            32   16.3    3.4    0.6    20.9           22.3         #>   M            26   15.0    3.7    0.7    24.7           25.6         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #>   F            32    0.0    0.0    0.0    20.5           24.8         #>   M            26    0.0    0.0    0.0    19.5           18.9         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #>   F            32    9.6    2.2    0.4    22.4           23.5         #>   M            26    9.6    1.9    0.4    19.7           19.5         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #>   F            32    3.0    0.7    0.1    24.7           25.9         #>   M            26    3.0    0.6    0.1    19.8           20.0         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4         #>   F            32    0.0    0.0    0.0    19.6           20.4         #>   M            26    0.0    0.0    0.0    18.0           17.6"},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add variable labels to top left corner in table — append_varlabels","title":"Add variable labels to top left corner in table — append_varlabels","text":"Helper layout-creating function append variable labels given variables vector given dataset top left corner. variable label found variable name used instead. Multiple variable labels concatenated slashes.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"append_varlabels(lyt, df, vars, indent = 0L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add variable labels to top left corner in table — append_varlabels","text":"lyt (PreDataTableLayouts) layout analyses added . df (data.frame) data set containing analysis variables. vars (character) variable names labels looked df. indent (integer(1)) non-negative number nested indent space, default 0L means indent. 1L means two spaces indent, 2L means four spaces indent .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add variable labels to top left corner in table — append_varlabels","text":"modified layout new variable label(s) added top-left material.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Add variable labels to top left corner in table — append_varlabels","text":"optimal implementation course, since using data set layout creation. mature rtables implementation also improved necessary anymore.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/append_varlabels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"SEX\") %>%   append_varlabels(DM, \"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, \"AGE\", indent = 1) build_table(lyt, DM) #> SEX                   A: Drug X          B: Placebo       C: Combination  #>   Age                  (N=121)            (N=106)            (N=129)      #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA         lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, c(\"SEX\", \"AGE\")) build_table(lyt, DM) #> SEX / Age             A: Drug X          B: Placebo       C: Combination  #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply automatic formatting — apply_auto_formatting","title":"Apply automatic formatting — apply_auto_formatting","text":"Checks listed formats .formats \"auto\", replaces \"auto\" correct implementation format_auto given statistics, data, variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply automatic formatting — apply_auto_formatting","text":"","code":"apply_auto_formatting(.formats, x_stats, .df_row, .var)"},{"path":"https://insightsengineering.github.io/tern/main/reference/apply_auto_formatting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply automatic formatting — apply_auto_formatting","text":".formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. x_stats (named list) named list statistics element corresponds element .formats, matching names. .df_row (data.frame) data frame across columns given row split. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard arguments — argument_convention","title":"Standard arguments — argument_convention","text":"documentation function lists arguments tern used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard arguments — argument_convention","text":"... additional arguments lower level functions. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .df_row (data.frame) data frame across columns given row split. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .ref_group (data.frame vector) data corresponding reference group. .spl_context (data.frame) gives information ancestor split states passed rtables. .stats (character) statistics select table. .var (string) single variable name passed rtables requested statistics function. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. col_by (factor) defining column groups. conf_level (proportion) confidence level interval. data (data.frame) dataset containing variables summarize. df (data.frame) data set containing analysis variables. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. id (string) subject variable name. is_event (flag)TRUE event, FALSE time event censored. label_all (string) label total population analysis. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. lyt (PreDataTableLayouts) layout analyses added . method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. na.rm (flag) whether NA values removed x prior analysis. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. prune_zero_rows (flag) whether prune zero rows. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. rsp (logical) vector indicating whether subject responder . show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. tte (numeric) vector time--event duration values. var_labels (character) variable labels. variables (named list string) list additional analysis variables. vars (character) variable names primary analysis variable iterated . var (string) single variable name primary analysis variable. x (numeric) vector numbers want analyze. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard arguments — argument_convention","text":"Although function just returns NULL two uses, tern users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple grobs — arrange_grobs","title":"Arrange multiple grobs — arrange_grobs","text":"Arrange grobs new grob n * m (rows * cols) layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"arrange_grobs(   ...,   grobs = list(...),   ncol = NULL,   nrow = NULL,   padding_ht = grid::unit(2, \"line\"),   padding_wt = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple grobs — arrange_grobs","text":"... grobs. grobs (list grob) list grobs. ncol (integer(1)) number columns layout. nrow (integer(1)) number rows layout. padding_ht (grid::unit) unit length 1, vertical space grob. padding_wt (grid::unit) unit length 1, horizontal space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple grobs — arrange_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/arrange_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"library(grid)  # \\donttest{ num <- lapply(1:9, textGrob) grid::grid.newpage() grid.draw(arrange_grobs(grobs = num, ncol = 2)) #> Warning: `arrange_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  showViewport()   g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, nrow = 2))  showViewport()   grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, ncol = 3))   grid::grid.newpage() grid::pushViewport(grid::viewport(layout = grid::grid.layout(1, 2))) vp1 <- grid::viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(arrange_grobs(g1, g2, g3, ncol = 2, vp = vp1))  showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to rtable — as.rtable","title":"Convert to rtable — as.rtable","text":"new generic function convert objects rtable tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to rtable — as.rtable","text":"","code":"as.rtable(x, ...)  # S3 method for class 'data.frame' as.rtable(x, format = \"xx.xx\", ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to rtable — as.rtable","text":"x (data.frame) object converted rtable. ... additional arguments methods. format (string function) format used columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to rtable — as.rtable","text":"rtables table object. Note concrete class depend method used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Convert to rtable — as.rtable","text":".rtable(data.frame): Method converting data.frame contains numeric columns rtable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as.rtable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert to rtable — as.rtable","text":"","code":"x <- data.frame(   a = 1:10,   b = rnorm(10) ) as.rtable(x) #>        a       b   #> —————————————————— #> 1    1.00    0.07  #> 2    2.00    -0.64 #> 3    3.00    -0.05 #> 4    4.00    -0.25 #> 5    5.00    0.44  #> 6    6.00    2.76  #> 7    7.00    0.05  #> 8    8.00    0.58  #> 9    9.00    0.12  #> 10   10.00   -1.91"},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of a vector to a factor — as_factor_keep_attributes","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"Converts x factor keeps attributes. Warns appropriately user can decide whether prefer converting factor manually (e.g. full control factor levels).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"","code":"as_factor_keep_attributes(   x,   x_name = deparse(substitute(x)),   na_level = \"<Missing>\",   verbose = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"x (vector) object convert. x_name (string) name x. na_level (string) explicit missing level used converting character vector. verbose (flag) defaults TRUE. prints warnings messages.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/as_factor_keep_attributes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"factor attributes (except class) x. modify x already factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional assertions to use with checkmate — assertions","title":"Additional assertions to use with checkmate — assertions","text":"Additional assertion functions can used together checkmate package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional assertions to use with checkmate — assertions","text":"","code":"assert_list_of_variables(x, .var.name = checkmate::vname(x), add = NULL)  assert_df_with_variables(   df,   variables,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_valid_factor(   x,   min.levels = 1,   max.levels = NULL,   null.ok = TRUE,   any.missing = TRUE,   n.levels = NULL,   len = NULL,   .var.name = checkmate::vname(x),   add = NULL )  assert_df_with_factors(   df,   variables,   min.levels = 1,   max.levels = NULL,   any.missing = TRUE,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_proportion_value(x, include_boundaries = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional assertions to use with checkmate — assertions","text":"x () object test. .var.name [character(1)] Name checked object print assertions. Defaults heuristic implemented vname. add [AssertCollection] Collection store assertion messages. See AssertCollection. df (data.frame) data set test. variables (named list character) list variables test. na_level (string) string using represent NA missing data. NA values please consider using directly .na() similar approaches. min.levels [integer(1)] Minimum number factor levels. Default NULL (check). max.levels [integer(1)] Maximum number factor levels. Default NULL (check). null.ok [logical(1)] set TRUE, x may also NULL. case type check x performed, additional checks disabled. .missing [logical(1)] vectors missing values allowed? Default TRUE. n.levels [integer(1)] Exact number factor levels. Default NULL (check). len [integer(1)] Exact expected length x. include_boundaries (flag) whether include boundaries testing proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional assertions to use with checkmate — assertions","text":"Nothing assertion passes, otherwise prints error message.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional assertions to use with checkmate — assertions","text":"assert_list_of_variables(): Checks whether x valid list variable names. NULL elements list x dropped Filter(Negate(.null), x). assert_df_with_variables(): Check whether df data frame analysis variables. Please notice produces error variables present data.frame opposite required. assert_valid_factor(): Check whether x valid factor (.e. levels empty string levels). Note NULL NA elements allowed. assert_df_with_factors(): Check whether df data frame analysis variables factors. Note creation NA direct call factor() trim NA levels vector list . assert_proportion_value(): Check whether x proportion: number 0 1.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for bins in percent — bins_percent_labels","title":"Labels for bins in percent — bins_percent_labels","text":"creates labels quantile based bins percent. assumes right-closed intervals produced cut_quantile_bins().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for bins in percent — bins_percent_labels","text":"","code":"bins_percent_labels(probs, digits = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for bins in percent — bins_percent_labels","text":"probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. digits (integer(1)) number decimal places round percent numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/bins_percent_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for bins in percent — bins_percent_labels","text":"character vector labels format [0%,20%], (20%,50%], etc.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add row total to labels — c_label_n","title":"Content row function to add row total to labels — c_label_n","text":"takes label latest row split level adds row total df parentheses. function differs c_label_n_alt() taking row counts df rather alt_counts_df, used add_rowcounts() alt_counts set FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add row total to labels — c_label_n","text":"","code":"c_label_n(df, labelstr, .N_row)"},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add row total to labels — c_label_n","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add row total to labels — c_label_n","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Content row function to add row total to labels — c_label_n","text":"important use df rather .N_row implementation, former already split columns refer first column data .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"takes label latest row split level adds row total alt_counts_df parentheses. function differs c_label_n() taking row counts alt_counts_df rather df, used add_rowcounts() alt_counts set TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"","code":"c_label_n_alt(df, labelstr, .alt_df_row)"},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/c_label_n_alt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor for content functions given a data frame with flag input — cfun_by_flag","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"can useful tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"","code":"cfun_by_flag(analysis_var, flag_var, format = \"xx\", .indent_mods = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"analysis_var (string) variable name column containing values returned content function. flag_var (string) variable name logical column identifying row returned. format (string)rtables format use.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cfun_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"content function gives df$analysis_var row identified .df_row$flag given format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Check proportion difference arguments — check_diff_prop_ci","title":"Check proportion difference arguments — check_diff_prop_ci","text":"Verifies /convert arguments valid values used estimation difference responder proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check proportion difference arguments — check_diff_prop_ci","text":"","code":"check_diff_prop_ci(rsp, grp, strata = NULL, conf_level, correct = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/check_diff_prop_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check proportion difference arguments — check_diff_prop_ci","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). strata (factor) variable one level per stratum length rsp. conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Check element dimension — check_same_n","title":"Check element dimension — check_same_n","text":"Checks elements ... dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check element dimension — check_same_n","text":"","code":"check_same_n(..., omit_null = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check element dimension — check_same_n","text":"... (data.frame vector) data frames vectors. omit_null (flag) whether NULL elements ... omitted check.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/check_same_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check element dimension — check_same_n","text":"logical value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Class for CombinationFunction — combination_function","title":"Class for CombinationFunction — combination_function","text":"CombinationFunction S4 class extends standard functions. special functions can combined negated logical operators.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Class for CombinationFunction — combination_function","text":"","code":"# S4 method for class 'CombinationFunction,CombinationFunction' e1 & e2  # S4 method for class 'CombinationFunction,CombinationFunction' e1 | e2  # S4 method for class 'CombinationFunction' !x"},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Class for CombinationFunction — combination_function","text":"e1 (CombinationFunction) left hand side logical operator. e2 (CombinationFunction) right hand side logical operator. x (CombinationFunction) function negated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Class for CombinationFunction — combination_function","text":"logical value indicating whether left hand side equation equals right hand side.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Class for CombinationFunction — combination_function","text":"e1 & e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. e1 | e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. `!`(CombinationFunction): Logical negation CombinationFunction functions. resulting object class, evaluates original function. result opposite results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combination_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Class for CombinationFunction — combination_function","text":"","code":"higher <- function(a) {   force(a)   CombinationFunction(     function(x) {       x > a     }   ) }  lower <- function(b) {   force(b)   CombinationFunction(     function(x) {       x < b     }   ) }  c1 <- higher(5) c2 <- lower(10) c3 <- higher(5) & lower(10) c3(7) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine counts — combine_counts","title":"Combine counts — combine_counts","text":"Simplifies estimation column counts, especially group combination required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine counts — combine_counts","text":"","code":"combine_counts(fct, groups_list = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine counts — combine_counts","text":"fct (factor) variable levels needs grouped. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine counts — combine_counts","text":"vector column counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine counts — combine_counts","text":"","code":"ref <- c(\"A: Drug X\", \"B: Placebo\") groups <- combine_groups(fct = DM$ARM, ref = ref)  col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> n                   227                 129       #> Mean (SD)        34.0 (7.2)          34.6 (6.5)   #> Median              33.0                33.0      #> Min - Max       20.0 - 60.0         22.0 - 53.0    ref <- \"A: Drug X\" groups <- combine_groups(fct = DM$ARM, ref = ref) col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>              A: Drug X    B: Placebo/C: Combination #>               (N=121)              (N=235)          #> ——————————————————————————————————————————————————— #> n               121                  235            #> Mean (SD)   34.9 (7.8)           33.9 (6.5)         #> Median         33.0                 33.0            #> Min - Max   20.0 - 60.0          21.0 - 55.0"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Reference and treatment group combination — combine_groups","title":"Reference and treatment group combination — combine_groups","text":"Facilitate re-combination groups divided reference treatment groups; helps arranging groups columns rtables framework teal modules.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reference and treatment group combination — combine_groups","text":"","code":"combine_groups(fct, ref = NULL, collapse = \"/\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reference and treatment group combination — combine_groups","text":"fct (factor) variable levels needs grouped. ref (character) reference level(s). collapse (string) character string separate fct ref.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reference and treatment group combination — combine_groups","text":"list first item ref (reference) second item trt (treatment).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reference and treatment group combination — combine_groups","text":"","code":"groups <- combine_groups(   fct = DM$ARM,   ref = c(\"B: Placebo\") )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM) #>             B: Placebo    A: Drug X/C: Combination #>               (N=106)             (N=250)          #> —————————————————————————————————————————————————— #> n               106                 250            #> Mean (SD)   33.0 (6.3)           34.7 (7.1)        #> Median         32.0                 33.0           #> Min - Max   21.0 - 55.0         20.0 - 60.0"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine factor levels — combine_levels","title":"Combine factor levels — combine_levels","text":"Combine specified old factor Levels single new level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine factor levels — combine_levels","text":"","code":"combine_levels(x, levels, new_level = paste(levels, collapse = \"/\"))"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine factor levels — combine_levels","text":"x (factor) factor variable. levels (character) level names combined. new_level (string) name new level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine factor levels — combine_levels","text":"factor new levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine factor levels — combine_levels","text":"","code":"x <- factor(letters[1:5], levels = letters[5:1]) combine_levels(x, levels = c(\"a\", \"b\")) #> [1] a/b a/b c   d   e   #> Levels: e d c a/b  combine_levels(x, c(\"e\", \"b\")) #> [1] a   e/b c   d   e/b #> Levels: e/b d c a"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Element-wise combination of two vectors — combine_vectors","title":"Element-wise combination of two vectors — combine_vectors","text":"Element-wise combination two vectors","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(x, y)"},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Element-wise combination of two vectors — combine_vectors","text":"x (vector) first vector combine. y (vector) second vector combine.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Element-wise combination of two vectors — combine_vectors","text":"list element combines corresponding elements x y.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/combine_vectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(1:3, 4:6) #> [[1]] #> [1] 1 4 #>  #> [[2]] #> [1] 2 5 #>  #> [[3]] #> [1] 3 6 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare variables between groups — compare_variables","title":"Compare variables between groups — compare_variables","text":"analyze function compare_vars() creates layout element summarize compare one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\", add_pval = TRUE) non-numeric variables running get_stats(\"analyze_vars_counts\", add_pval = TRUE). Use .stats parameter specify statistics include output summary table. Prior using function table layout must use rtables::split_cols_by() create column split variable used comparisons, specify reference group via ref_group parameter. Comparisons can performed group (column) specified reference group including p-value statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare variables between groups — compare_variables","text":"","code":"compare_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"count_fraction\", \"pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'numeric' s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'factor' s_compare(x, .ref_group, .in_ref_col, denom = \"n\", na.rm = TRUE, ...)  # S3 method for class 'character' s_compare(   x,   .ref_group,   .in_ref_col,   denom = \"n\",   na.rm = TRUE,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_compare(x, .ref_group, .in_ref_col, na.rm = TRUE, denom = \"n\", ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare variables between groups — compare_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_compare(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Run get_stats(\"analyze_vars_numeric\", add_pval = TRUE) see statistics available numeric variables, get_stats(\"analyze_vars_counts\", add_pval = TRUE) statistics available non-numeric variables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. denom (string) choice denominator factor proportions, can n (number values row column intersection). .var (string) single variable name passed rtables requested statistics function. verbose (flag) whether warnings messages printed. Mainly used print information factor casting. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare variables between groups — compare_variables","text":"compare_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_compare() table layout. s_compare() returns output s_summary() comparisons versus reference group form p-values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Compare variables between groups — compare_variables","text":"compare_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_compare(): S3 generic function produce comparison summary. s_compare(numeric): Method numeric class. uses standard t-test calculate p-value. s_compare(factor): Method factor class. uses chi-squared test calculate p-value. s_compare(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_compare(logical): Method logical class. chi-squared test used. missing values removed, counted FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Compare variables between groups — compare_variables","text":"factor variables, denom factor proportions can n since purpose compare proportions columns, therefore row-based proportion make sense. Proportion based N_col difficult since use counts chi-squared test statistic, therefore missing values accounted explicit factor levels. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. character variables, automatic conversion factor guarantee table generated correctly. particular sparse tables likely can fail. Therefore always better manually convert character variables factors pre-processing. compare_vars(), column split must define reference group via ref_group comparison well defined.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/compare_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare variables between groups — compare_variables","text":"","code":"# `compare_vars()` in `rtables` pipelines  ## Default output within a `rtables` pipeline. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM B\") %>%   compare_vars(c(\"AGE\", \"SEX\")) build_table(lyt, tern_ex_adsl) #>                                  ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————— #> AGE                                                                 #>   n                                69           73           58     #>   Mean (SD)                    34.1 (6.8)   35.8 (7.1)   36.1 (7.4) #>   p-value (t-test)               0.1446                    0.8212   #> SEX                                                                 #>   n                                69           73           58     #>   F                            38 (55.1%)   40 (54.8%)   32 (55.2%) #>   M                            31 (44.9%)   33 (45.2%)   26 (44.8%) #>   p-value (chi-squared test)     1.0000                    1.0000    ## Select and format statistics output. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM C\") %>%   compare_vars(     vars = \"AGE\",     .stats = c(\"mean_sd\", \"pval\"),     .formats = c(mean_sd = \"xx.x, xx.x\"),     .labels = c(mean_sd = \"Mean, SD\")   ) build_table(lyt, df = tern_ex_adsl) #>                      ARM A       ARM B       ARM C   #> ———————————————————————————————————————————————————— #> Mean, SD           34.1, 6.8   35.8, 7.1   36.1, 7.4 #> p-value (t-test)    0.1176      0.8212                # `s_compare.numeric`  ## Usual case where both this and the reference group vector have more than 1 value. s_compare(rnorm(10, 5, 1), .ref_group = rnorm(5, -5, 1), .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 51.27191  #>  #> $mean #>     mean  #> 5.127191  #>  #> $sd #>       sd  #> 1.226119  #>  #> $se #>       se  #> 0.387733  #>  #> $mean_sd #>     mean       sd  #> 5.127191 1.226119  #>  #> $mean_se #>     mean       se  #> 5.127191 0.387733  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.739458     5.514924  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.901071     6.353310  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>      p_value  #> 3.353908e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.024369  #>  #> $mad #>           mad  #> -4.440892e-16  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      4.638779      5.862086  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.756763      5.549828  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>       iqr  #> 0.7930643  #>  #> $range #>      min      max  #> 2.725885 7.682557  #>  #> $min #>      min  #> 2.725885  #>  #> $max #>      max  #> 7.682557  #>  #> $median_range #>   median      min      max  #> 5.024369 2.725885 7.682557  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 23.91406  #>  #> $geom_mean #> geom_mean  #>  4.985435  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 26.26258  #>  #> $pval #> [1] 2.25779e-08 #>   ## If one group has not more than 1 value, then p-value is not calculated. s_compare(rnorm(10, 5, 1), .ref_group = 1, .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 50.71578  #>  #> $mean #>     mean  #> 5.071578  #>  #> $sd #>       sd  #> 1.105832  #>  #> $se #>        se  #> 0.3496948  #>  #> $mean_sd #>     mean       sd  #> 5.071578 1.105832  #>  #> $mean_se #>      mean        se  #> 5.0715780 0.3496948  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.721883     5.421273  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.965746     6.177410  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>      p_value  #> 1.511204e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.260423  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      3.529264      6.318293  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.024149      6.065057  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>      iqr  #> 2.040908  #>  #> $range #>      min      max  #> 3.300549 6.337320  #>  #> $min #>      min  #> 3.300549  #>  #> $max #>     max  #> 6.33732  #>  #> $median_range #>   median      min      max  #> 5.260423 3.300549 6.337320  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>      cv  #> 21.8045  #>  #> $geom_mean #> geom_mean  #>  4.952266  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 23.97201  #>  #> $pval #> character(0) #>   ## Empty numeric does not fail, it returns NA-filled items and no p-value. s_compare(numeric(), .ref_group = numeric(), .in_ref_col = FALSE) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $pval #> character(0) #>   # `s_compare.factor`  ## Basic usage: x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) y <- factor(c(\"a\", \"b\", \"c\")) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Management of NA values. x <- explicit_na(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\", NA, NA))) y <- explicit_na(factor(c(\"a\", \"b\", \"c\", NA))) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 7 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 2 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0000000 0.4285714 #>  #> $count_fraction$b #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$c #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$`<Missing>` #> [1] 2.0000000 0.2857143 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     7  #>  #> $fraction$b #>   num denom  #>     1     7  #>  #> $fraction$c #>   num denom  #>     1     7  #>  #> $fraction$`<Missing>` #>   num denom  #>     2     7  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.9063036 #>   # `s_compare.character`  ## Basic usage: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\") y <- c(\"a\", \"b\", \"c\") s_compare(x, .ref_group = y, .in_ref_col = FALSE, .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Note that missing values handling can make a large difference: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\", NA) y <- c(\"a\", \"b\", \"c\", rep(NA, 20)) s_compare(x,   .ref_group = y, .in_ref_col = FALSE,   .var = \"x\", verbose = FALSE ) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x,   .ref_group = y, .in_ref_col = FALSE, .var = \"x\",   na.rm = FALSE, verbose = FALSE ) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`<Missing>` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.005768471 #>   # `s_compare.logical`  ## Basic usage: x <- c(TRUE, FALSE, TRUE, TRUE) y <- c(FALSE, FALSE, TRUE) s_compare(x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.2702894 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) y <- c(NA, NA, NA, NA, FALSE) s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.3864762 #>  s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.1675463 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for descriptive statistics — control_analyze_vars","title":"Control function for descriptive statistics — control_analyze_vars","text":"Sets list parameters summaries descriptive statistics. Typically used internally specify details s_summary(). function family mainly used analyze_vars().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for descriptive statistics — control_analyze_vars","text":"","code":"control_analyze_vars(   conf_level = 0.95,   quantiles = c(0.25, 0.75),   quantile_type = 2,   test_mean = 0 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for descriptive statistics — control_analyze_vars","text":"conf_level (proportion) confidence level interval. quantiles (numeric(2)) vector length two specify quantiles calculate. quantile_type (numeric(1)) number 1 9 selecting quantile algorithms used. Default set 2 matches default quantile algorithm SAS proc univariate set QNTLDEF=5. differs R's default. See type stats::quantile(). test_mean (numeric(1)) number test mean null hypothesis calculating p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_analyze_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for descriptive statistics — control_analyze_vars","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Control functions for Kaplan-Meier plot annotation tables — control_annot","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"Auxiliary functions controlling arguments formatting annotation tables can added plots generated via g_km().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot(x = 0.8, y = 0.85, w = 0.32, h = 0.16, fill = TRUE)  control_coxph_annot(   x = 0.29,   y = 0.51,   w = 0.4,   h = 0.125,   fill = TRUE,   ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"x (proportion) x-coordinate center annotation table. y (proportion) y-coordinate center annotation table. w (proportion) relative width annotation table. h (proportion) relative height annotation table. fill (flag character) whether annotation table background fill color. Can also color code use background fill color. TRUE, color code defaults \"#00000020\". ref_lbls (flag) whether reference group explicitly printed labels annotation table. FALSE (default), comparison groups printed table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"control_surv_med_annot(): Control function formatting median survival time annotation table. annotation table can added g_km() setting annot_surv_med=TRUE, can configured using control_surv_med_annot() function setting control_annot_surv_med argument. control_coxph_annot(): Control function formatting Cox-PH annotation table. annotation table can added g_km() setting annot_coxph=TRUE, can configured using control_coxph_annot() function setting control_annot_coxph argument.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot() #> $x #> [1] 0.8 #>  #> $y #> [1] 0.85 #>  #> $w #> [1] 0.32 #>  #> $h #> [1] 0.16 #>  #> $fill #> [1] TRUE #>   control_coxph_annot() #> $x #> [1] 0.29 #>  #> $y #> [1] 0.51 #>  #> $w #> [1] 0.4 #>  #> $h #> [1] 0.125 #>  #> $fill #> [1] TRUE #>  #> $ref_lbls #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox-PH model — control_coxph","title":"Control function for Cox-PH model — control_coxph","text":"auxiliary function controlling arguments Cox-PH model, typically used internally specify details Cox-PH model s_coxph_pairwise(). conf_level refers Hazard Ratio estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox-PH model — control_coxph","text":"","code":"control_coxph(   pval_method = c(\"log-rank\", \"wald\", \"likelihood\"),   ties = c(\"efron\", \"breslow\", \"exact\"),   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox-PH model — control_coxph","text":"pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) string specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox-PH model — control_coxph","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox regression — control_coxreg","title":"Control function for Cox regression — control_coxreg","text":"Sets list parameters Cox regression fit. Used internally.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg(   pval_method = c(\"wald\", \"likelihood\"),   ties = c(\"exact\", \"efron\", \"breslow\"),   conf_level = 0.95,   interaction = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox regression — control_coxreg","text":"pval_method (string) method used estimation p.values; wald (default) likelihood. ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. conf_level (proportion) confidence level interval. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox regression — control_coxreg","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg() #> $pval_method #> [1] \"wald\" #>  #> $ties #> [1] \"exact\" #>  #> $conf_level #> [1] 0.95 #>  #> $interaction #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for incidence rate — control_incidence_rate","title":"Control function for incidence rate — control_incidence_rate","text":"auxiliary function controlling arguments incidence rate, used internally specify details s_incidence_rate().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(   conf_level = 0.95,   conf_type = c(\"normal\", \"normal_log\", \"exact\", \"byar\"),   input_time_unit = c(\"year\", \"day\", \"week\", \"month\"),   num_pt_year = 100 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for incidence rate — control_incidence_rate","text":"conf_level (proportion) confidence level interval. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric(1)) number patient-years use calculating adverse event rates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for incidence rate — control_incidence_rate","text":"list components names arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(0.9, \"exact\", \"month\", 100) #> $conf_level #> [1] 0.9 #>  #> $conf_type #> [1] \"exact\" #>  #> $input_time_unit #> [1] \"month\" #>  #> $num_pt_year #> [1] 100 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for g_lineplot() — control_lineplot_vars","title":"Control function for g_lineplot() — control_lineplot_vars","text":"Default values variables parameter g_lineplot function. variable's default value can overwritten variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars(   x = \"AVISIT\",   y = \"AVAL\",   group_var = \"ARM\",   facet_var = NA,   paramcd = \"PARAMCD\",   y_unit = \"AVALU\",   subject_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for g_lineplot() — control_lineplot_vars","text":"x (string) x-variable name. y (string) y-variable name. group_var (string NA) group variable name. facet_var (string NA) faceting variable name. paramcd (string NA) parameter code variable name. y_unit (string NA) y-axis unit variable name. subject_var (string NA) subject variable name.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for g_lineplot() — control_lineplot_vars","text":"named character vector variable names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_lineplot_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars() #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"       \"ARM\"   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA  control_lineplot_vars(group_var = NA) #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"          NA   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for logistic regression model fitting — control_logistic","title":"Control function for logistic regression model fitting — control_logistic","text":"auxiliary function controlling arguments logistic regression models. conf_level refers confidence level used Odds Ratio CIs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"control_logistic(response_definition = \"response\", conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for logistic regression model fitting — control_logistic","text":"response_definition (string) definition event terms response. used fitting logistic regression model left hand side formula. Note evaluated expression result either logical vector factor 2 levels. default just \"response\" original response variable used modified . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for logistic regression model fitting — control_logistic","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"# Standard options. control_logistic() #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.95 #>   # Modify confidence level. control_logistic(conf_level = 0.9) #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.9 #>   # Use a different response definition. control_logistic(response_definition = \"I(response %in% c('CR', 'PR'))\") #> $response_definition #> [1] \"I(response %in% c('CR', 'PR'))\" #>  #> $conf_level #> [1] 0.95 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for risk difference column — control_riskdiff","title":"Control function for risk difference column — control_riskdiff","text":"Sets list parameters use generating risk (proportion) difference column. Used input riskdiff parameter tabulate_rsp_subgroups() tabulate_survival_subgroups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff(   arm_x = NULL,   arm_y = NULL,   format = \"xx.x (xx.x - xx.x)\",   col_label = \"Risk Difference (%) (95% CI)\",   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for risk difference column — control_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. format (string function) format label (string) formatting function apply risk difference statistic. See 3d string options formatters::list_valid_format_labels() possible format strings. Defaults \"xx.x (xx.x - xx.x)\". col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for risk difference column — control_riskdiff","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/control_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff() #> $arm_x #> NULL #>  #> $arm_y #> NULL #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>  control_riskdiff(arm_x = \"ARM A\", arm_y = \"ARM B\") #> $arm_x #> [1] \"ARM A\" #>  #> $arm_y #> [1] \"ARM B\" #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"auxiliary function controlling arguments STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"control_step(   biomarker = NULL,   use_percentile = TRUE,   bandwidth,   degree = 0L,   num_points = 39L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"biomarker (numeric NULL) optional provision numeric biomarker variable, used infer bandwidth, see . use_percentile (flag) TRUE, running windows created according quantiles rather actual values, .e. bandwidth refers percentage data covered window. Suggest TRUE biomarker variable uniformly distributed. bandwidth (numeric(1) NULL) indicating bandwidth window. Depending argument use_percentile, can either length actual-value windows real biomarker scale, percentage windows. use_percentile = TRUE, number 0 1. NULL, treat bandwidth infinity, means one global model fitted. default, 0.25 used percentage windows one quarter range biomarker variable actual-value windows. degree (integer(1)) degree polynomial function biomarker interaction term treatment arm fitted window. 0 (default), biomarker variable included model fitted biomarker window. num_points (integer(1)) number points hazard ratios estimated. smallest number 2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"list components names arguments, except biomarker just used calculate bandwidth case actual biomarker windows requested.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"# Provide biomarker values and request actual values to be used, # so that bandwidth is chosen from range. control_step(biomarker = 1:10, use_percentile = FALSE) #> $use_percentile #> [1] FALSE #>  #> $bandwidth #> [1] 2.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 39 #>   # Use a global model with quadratic biomarker interaction term. control_step(bandwidth = NULL, degree = 2) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> NULL #>  #> $degree #> [1] 2 #>  #> $num_points #> [1] 39 #>   # Reduce number of points to be used. control_step(num_points = 10) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> [1] 0.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 10 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for survival time — control_surv_time","title":"Control function for survfit models for survival time — control_surv_time","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_time(). conf_level refers survival time estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for survival time — control_surv_time","text":"","code":"control_surv_time(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\"),   quantiles = c(0.25, 0.75) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for survival time — control_surv_time","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. quantiles (numeric(2)) vector length two specifying quantiles survival time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for survival time — control_surv_time","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_timepoint(). conf_level refers patient risk estimation time point.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"","code":"control_surv_timepoint(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/control_surv_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative counts of numeric variable by thresholds — count_cumulative","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"analyze function count_cumulative() creates layout element calculate cumulative counts values numeric variable less , less equal , greater , greater equal user-specified threshold values. function analyzes numeric variable vars threshold values supplied thresholds argument numeric vector. Whether counts include threshold values, whether count values lower higher threshold values can set via include_eq lower_tail parameters, respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"count_cumulative(   lyt,   vars,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   ... )  a_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) vector cutoff values counts. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_cumulative\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_cumulative() table layout. s_count_cumulative() returns named list count_fractions: list thresholds value component, component containing vector count fraction. a_count_cumulative() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_cumulative(): Statistics function produces named list given numeric vector thresholds. a_count_cumulative(): Formatted analysis function used afun count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_cumulative(     vars = \"AGE\",     thresholds = c(40, 60)   ) %>%   build_table(tern_ex_adsl) #>           A: Drug X    B: Placebo   C: Combination #>             (N=69)       (N=73)         (N=58)     #> —————————————————————————————————————————————————— #> AGE                                                #>   <= 40   52 (75.4%)   58 (79.5%)     41 (70.7%)   #>   <= 60   69 (100%)    73 (100%)      58 (100%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients with missed doses by thresholds — count_missed_doses","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"analyze function creates layout element calculate cumulative counts patients number missed doses least equal user-specified threshold values. function analyzes numeric variable vars, variable numbers missed doses, threshold values supplied thresholds argument numeric vector. function assumes every row given data frame corresponds unique patient.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"count_missed_doses(   lyt,   vars,   thresholds,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_nonmissing(x)  s_count_missed_doses(x, thresholds, .N_col)  a_count_missed_doses(x, thresholds, .N_col)"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) minimum number missed doses patients . var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_missed_doses\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_missed_doses() table layout. s_count_nonmissing() returns statistic n count non-missing values x. s_count_missed_doses() returns statistics n count_fraction one element threshold. a_count_missed_doses() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_nonmissing(): Statistics function count non-missing values. s_count_missed_doses(): Statistics function count patients missed doses. a_count_missed_doses(): Formatted analysis function used afun count_missed_doses().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_missed_doses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"library(dplyr)  anl <- tern_ex_adsl %>%   distinct(STUDYID, USUBJID, ARM) %>%   mutate(     PARAMCD = \"TNDOSMIS\",     PARAM = \"Total number of missed doses during study\",     AVAL = sample(0:20, size = nrow(tern_ex_adsl), replace = TRUE),     AVALC = \"\"   )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_missed_doses(\"AVAL\", thresholds = c(1, 5, 10, 15), var_labels = \"Missed Doses\") %>%   build_table(anl, alt_counts_df = tern_ex_adsl) #>                              A: Drug X    B: Placebo   C: Combination #>                                (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————— #> Missed Doses                                                          #>   n                              69           73             58       #>   At least 1 missed dose     69 (100%)    69 (94.5%)     55 (94.8%)   #>   At least 5 missed doses    57 (82.6%)   55 (75.3%)     50 (86.2%)   #>   At least 10 missed doses    40 (58%)    40 (54.8%)     32 (55.2%)   #>   At least 15 missed doses   26 (37.7%)   25 (34.2%)     13 (22.4%)"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences — count_occurrences","title":"Count occurrences — count_occurrences","text":"analyze function count_occurrences() creates layout element calculate occurrence counts patients. function analyzes variable(s) supplied vars returns table occurrence counts unique value (level) variable(s). variable (variables) must non-numeric. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences value recorded patient, value counted . summarize function summarize_occurrences() performs function count_occurrences() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences — count_occurrences","text":"","code":"count_occurrences(   lyt,   vars,   id = \"USUBJID\",   drop = TRUE,   var_labels = vars,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  summarize_occurrences(   lyt,   var,   id = \"USUBJID\",   drop = TRUE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences(   df,   denom = c(\"N_col\", \"n\"),   .N_col,   .df_row,   drop = TRUE,   .var = \"MHDECOD\",   id = \"USUBJID\" )  a_count_occurrences(   df,   labelstr = \"\",   id = \"USUBJID\",   denom = c(\"N_col\", \"n\"),   drop = TRUE,   .N_col,   .var = NULL,   .df_row = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences — count_occurrences","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . id (string) subject variable name. drop (flag) whether non-appearing occurrence levels dropped resulting table. Note case remaining occurrence levels table sorted alphabetically. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_occurrences\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. denom (string) choice denominator patient proportions. Can : N_col: total number patients column across rows n: number patients occurrences .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .df_row (data.frame) data frame across columns given row split. .var, var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences — count_occurrences","text":"count_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences() table layout. summarize_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences() table layout. s_count_occurrences() returns list : count: list counts one element per occurrence. count_fraction: list counts fractions one element per occurrence. fraction: list numerators denominators one element per occurrence. a_count_occurrences() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences — count_occurrences","text":"count_occurrences(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences(): Statistics function counts number patients report occurrence. a_count_occurrences(): Formatted analysis function used afun count_occurrences().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count occurrences — count_occurrences","text":"default, occurrences appear given row split dropped table occurrences table sorted alphabetically per row split. Therefore, corresponding layout needs use split_fun = drop_split_levels split_rows_by calls. Use drop = FALSE like show occurrences.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences — count_occurrences","text":"","code":"library(dplyr) df <- data.frame(   USUBJID = as.character(c(     1, 1, 2, 4, 4, 4,     6, 6, 6, 7, 7, 8   )),   MHDECOD = c(     \"MH1\", \"MH2\", \"MH1\", \"MH1\", \"MH1\", \"MH3\",     \"MH2\", \"MH2\", \"MH3\", \"MH1\", \"MH2\", \"MH4\"   ),   ARM = rep(c(\"A\", \"B\"), each = 6),   SEX = c(\"F\", \"F\", \"M\", \"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\") ) df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Create table layout lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences(vars = \"MHDECOD\", .stats = c(\"count_fraction\"))  # Apply table layout to data and produce `rtable` object tbl <- lyt %>%   build_table(df, alt_counts_df = df_adsl) %>%   prune_table()  tbl #>           A           B     #>         (N=3)       (N=3)   #> ——————————————————————————— #> MH1   3 (100%)    1 (33.3%) #> MH2   1 (33.3%)   2 (66.7%) #> MH3   1 (33.3%)   1 (33.3%) #> MH4       0       1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"SEX\", child_labels = \"visible\") %>%   summarize_occurrences(     var = \"MHDECOD\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>          all obs  #>           (N=6)   #> ————————————————— #> F                 #>   MH1   1 (16.7%) #>   MH2   2 (33.3%) #>   MH3   1 (16.7%) #>   MH4   1 (16.7%) #> M                 #>   MH1   3 (50.0%) #>   MH2   1 (16.7%) #>   MH3   1 (16.7%)  # Count unique occurrences per subject. s_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> $count #> $count$MH1 #> [1] 4 #>  #> $count$MH2 #> [1] 3 #>  #> $count$MH3 #> [1] 2 #>  #> $count$MH4 #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$MH1 #> [1] 4 1 #>  #> $count_fraction$MH2 #> [1] 3.00 0.75 #>  #> $count_fraction$MH3 #> [1] 2.0 0.5 #>  #> $count_fraction$MH4 #> [1] 1.00 0.25 #>  #>  #> $fraction #> $fraction$MH1 #>   num denom  #>     4     4  #>  #> $fraction$MH2 #>   num denom  #>     3     4  #>  #> $fraction$MH3 #>   num denom  #>     2     4  #>  #> $fraction$MH4 #>   num denom  #>     1     4  #>  #>   a_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       MH1              4          0       MH1 #> 2       MH2              3          0       MH2 #> 3       MH3              2          0       MH3 #> 4       MH4              1          0       MH4 #> 5       MH1       4 (100%)          0       MH1 #> 6       MH2        3 (75%)          0       MH2 #> 7       MH3        2 (50%)          0       MH3 #> 8       MH4        1 (25%)          0       MH4 #> 9       MH1       4 (100%)          0       MH1 #> 10      MH2      3 (75.0%)          0       MH2 #> 11      MH3      2 (50.0%)          0       MH3 #> 12      MH4      1 (25.0%)          0       MH4 #> 13      MH1   4/4 (100.0%)          0       MH1 #> 14      MH2    3/4 (75.0%)          0       MH2 #> 15      MH3    2/4 (50.0%)          0       MH3 #> 16      MH4    1/4 (25.0%)          0       MH4"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences by grade — count_occurrences_by_grade","title":"Count occurrences by grade — count_occurrences_by_grade","text":"analyze function count_occurrences_by_grade() creates layout element calculate occurrence counts grade. function analyzes primary analysis variable var indicates toxicity grades. id variable used indicate unique subject identifiers (defaults USUBJID). user can also supply list custom groups grades analyze via grade_groups parameter. remove_single  argument remove single grades analysis grade groups analyzed. multiple grades recorded one patient highest grade level counted. summarize function summarize_occurrences_by_grade() performs function count_occurrences_by_grade() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"count_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   var_labels = var,   show_labels = \"default\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  summarize_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   na_str = default_na_str(),   ...,   .stats = NULL,   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences_by_grade(   df,   .var,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   labelstr = \"\" )  a_count_occurrences_by_grade(   df,   .var,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   labelstr = \"\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences by grade — count_occurrences_by_grade","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. grade_groups (named list character) list containing groupings grades. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE). var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_occurrences_by_grade\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences_by_grade() table layout. summarize_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences_by_grade() table layout. s_count_occurrences_by_grade() returns list counts fractions one element per grade level grade level grouping. a_count_occurrences_by_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences_by_grade(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences_by_grade(): Statistics function counts number patients highest grade. a_count_occurrences_by_grade(): Formatted analysis function used afun count_occurrences_by_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_occurrences_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(1:6, 1)),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"A\"), levels = c(\"A\", \"B\")),   AETOXGR = factor(c(1, 2, 3, 4, 1, 2, 3), levels = c(1:5)),   AESEV = factor(     x = c(\"MILD\", \"MODERATE\", \"SEVERE\", \"MILD\", \"MILD\", \"MODERATE\", \"SEVERE\"),     levels = c(\"MILD\", \"MODERATE\", \"SEVERE\")   ),   stringsAsFactors = FALSE )  df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Layout creating function with custom format. basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                  A               B       #>                (N=3)           (N=3)     #> ———————————————————————————————————————— #> MILD       0.00 (0.00%)    2.00 (66.67%) #> MODERATE   1.00 (33.33%)   1.00 (33.33%) #> SEVERE     2.00 (66.67%)   0.00 (0.00%)   # Define additional grade groupings. grade_groups <- list(   \"-Any-\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 1-2\" = c(\"1\", \"2\"),   \"Grade 3-5\" = c(\"3\", \"4\", \"5\") )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups,     only_grade_groups = TRUE   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 A           B     #>               (N=3)       (N=3)   #> ————————————————————————————————— #> -Any-       3 (100%)    3 (100%)  #> Grade 1-2   1 (33.3%)   2 (66.7%) #> Grade 3-5   2 (66.7%)   1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 all obs    #>                  (N=6)     #> —————————————————————————— #> A                          #>   MILD       0.00 (0.00%)  #>   MODERATE   1.00 (16.67%) #>   SEVERE     2.00 (33.33%) #> B                          #>   MILD       2.00 (33.33%) #>   MODERATE   1.00 (16.67%) #>   SEVERE     0.00 (0.00%)   basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                all obs  #>                 (N=6)   #> ——————————————————————— #> A                       #>   -Any-       3 (50.0%) #>   Grade 1-2   1 (16.7%) #>   1               0     #>   2           1 (16.7%) #>   Grade 3-5   2 (33.3%) #>   3           2 (33.3%) #>   4               0     #>   5               0     #> B                       #>   -Any-       3 (50.0%) #>   Grade 1-2   2 (33.3%) #>   1           1 (16.7%) #>   2           1 (16.7%) #>   Grade 3-5   1 (16.7%) #>   3               0     #>   4           1 (16.7%) #>   5               0      s_count_occurrences_by_grade(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> $count_fraction #> $count_fraction$ANY #> [1] 6.0 0.6 #>  #> $count_fraction$`1` #> [1] 1.0 0.1 #>  #> $count_fraction$`2` #> [1] 2.0 0.2 #>  #> $count_fraction$`3` #> [1] 2.0 0.2 #>  #> $count_fraction$`4` #> [1] 1.0 0.1 #>  #> $count_fraction$`5` #> [1] 0 0 #>  #>   #  We need to ungroup `count_fraction` first so that the `rtables` formatting # function `format_count_fraction()` can be applied correctly. afun <- make_afun(a_count_occurrences_by_grade, .ungroup_stats = \"count_fraction\") afun(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1      ANY      6 (60.0%)          0       ANY #> 2        1      1 (10.0%)          0         1 #> 3        2      2 (20.0%)          0         2 #> 4        3      2 (20.0%)          0         3 #> 5        4      1 (10.0%)          0         4 #> 6        5              0          0         5"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patient events in columns — count_patients_events_in_cols","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize function summarize_patients_events_in_cols() creates layout element summarize patient event counts columns. function analyzes elements (events) supplied via filters_list parameter returns row counts number patients event well total numbers patients events. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences event recorded patient, event counted .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"summarize_patients_events_in_cols(   lyt,   id = \"USUBJID\",   filters_list = list(),   empty_stats = character(),   na_str = default_na_str(),   ...,   .stats = c(\"unique\", \"all\", names(filters_list)),   .labels = c(unique = \"Patients (All)\", all = \"Events (All)\",     labels_or_names(filters_list)),   col_split = TRUE )  s_count_patients_and_multiple_events(   df,   id,   filters_list,   empty_stats = character(),   labelstr = \"\",   custom_label = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patient events in columns — count_patients_events_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. filters_list (named list character) list element list describes one type event describe filters, format s_count_patients_with_event(). label, used column title. empty_stats (character) optional names statistics returned empty corresponding table cells stay blank. na_str (string) string used replace NA empty values output. ... additional arguments lower level functions. .stats (character) statistics select table. Run get_stats(\"summarize_patients_events_in_cols\") see available statistics function, addition added using filters_list. .labels (named character) labels statistics (without indent). col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. custom_label (string NULL) provided labelstr empty used label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_patients_and_multiple_events() table layout. s_count_patients_and_multiple_events() returns list statistics: unique: number unique patients df. : number rows df. one element name filters_list: number rows df, .e. events, fulfilling filter condition.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_patients_and_multiple_events(): Statistics function counts numbers patients multiple events defined filters. Used analysis function afun summarize_patients_events_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_events_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"df <- data.frame(   USUBJID = rep(c(\"id1\", \"id2\", \"id3\", \"id4\"), c(2, 3, 1, 1)),   ARM = c(\"A\", \"A\", \"B\", \"B\", \"B\", \"B\", \"A\"),   AESER = rep(\"Y\", 7),   AESDTH = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"N\"),   AEREL = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"Y\"),   AEDECOD = c(\"A\", \"A\", \"A\", \"B\", \"B\", \"C\", \"D\"),   AEBODSYS = rep(c(\"SOC1\", \"SOC2\", \"SOC3\"), c(3, 3, 1)) )  # `summarize_patients_events_in_cols()` basic_table() %>%   summarize_patients_events_in_cols(     filters_list = list(       related = formatters::with_label(c(AEREL = \"Y\"), \"Events (Related)\"),       fatal = c(AESDTH = \"Y\"),       fatal_related = c(AEREL = \"Y\", AESDTH = \"Y\")     ),     custom_label = \"%s Total number of patients and events\"   ) %>%   build_table(df) #>                                          Patients (All)   Events (All)   Events (Related)   fatal   fatal_related #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> %s Total number of patients and events         4               7                5             4           4"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with a particular event — count_patients_with_event","title":"Count the number of patients with a particular event — count_patients_with_event","text":"analyze function count_patients_with_event() creates layout element calculate patient counts user-specified set events. function analyzes primary analysis variable vars indicates unique subject identifiers. Events defined user named vector via filters argument, name corresponds variable value value(s) variable takes event. multiple records event recorded patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"count_patients_with_event(   lyt,   vars,   filters,   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  a_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with a particular event — count_patients_with_event","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . filters (character) character vector specifying column names flag variables used counting number unique identifiers satisfying conditions. Multiple column names flags accepted format c(\"column_name1\" = \"flag1\", \"column_name2\" = \"flag2\"). Note equality accepted condition. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_patients_with_event\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_event() table layout. s_count_patients_with_event() returns count fraction unique identifiers defined event. a_count_patients_with_event() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_event(): Statistics function counts number patients defined event occurred. a_count_patients_with_event(): Formatted analysis function used afun count_patients_with_event().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_event.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"# `count_patients_with_event()`  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_values(     \"STUDYID\",     values = \"AB12345\",     .stats = \"count\",     .labels = c(count = \"Total AEs\")   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with at least one adverse event\"),     table_names = \"tbl_all\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),     .labels = c(count_fraction = \"Total number of patients with fatal AEs\"),     table_names = \"tbl_fatal\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\", \"AEREL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with related fatal AEs\"),     .indent_mods = c(count_fraction = 2L),     table_names = \"tbl_rel_fatal\"   )  build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                     202          177            162       #> Total number of patients with at least one adverse event   59 (100%)    57 (100%)      48 (100%)    #> Total number of patients with fatal AEs                    28 (47.5%)   31 (54.4%)     20 (41.7%)   #>     Total number of patients with related fatal AEs        28 (47.5%)   31 (54.4%)     20 (41.7%)    # `s_count_patients_with_event()`  s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\") ) #> $n #> [1] 164 #>  #> $count #> [1] 164 #>  #> $count_fraction #> [1] 164   1 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\") ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.4817073 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),   denom = \"N_col\",   .N_col = 456 ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.1732456 #>  #> $n_blq #> [1] 0 #>   # `a_count_patients_with_event()`  a_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\"),   .N_col = 100,   .N_row = 100 ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n            164          0              n #> 2          count            164          0          count #> 3 count_fraction     164 (100%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with particular flags — count_patients_with_flags","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"analyze function count_patients_with_flags() creates layout element calculate counts patients user-specified flags present. function analyzes primary analysis variable var indicates unique subject identifiers. Flags variables analyze specified user via flag_variables argument, must either take value TRUE (flag present) FALSE (flag absent) record. multiple records flag present patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"count_patients_with_flags(   lyt,   var,   flag_variables,   flag_labels = NULL,   var_labels = var,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = paste0(\"tbl_flags_\", var),   .stats = \"count_fraction\",   .formats = NULL,   .indent_mods = NULL )  s_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  a_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. flag_variables (character) vector specifying names logical variables analysis dataset used counting number unique identifiers. flag_labels (character) vector labels use flag variables. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_patients_with_flags\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_flags() table layout. s_count_patients_with_flags() returns count fraction unique identifiers particular flag list statistics n, count, count_fraction, n_blq, one element per flag. a_count_patients_with_flags() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_flags(): Statistics function counts number patients particular flag variable TRUE. a_count_patients_with_flags(): Formatted analysis function used afun count_patients_with_flags().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"flag_labels specified, variables labels extracted df. variables labeled, variable names used instead. Alternatively, named vector can supplied flag_variables within name-value pair name corresponds variable name value label use variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/count_patients_with_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"library(dplyr)  # Add labelled flag variables to analysis dataset. adae <- tern_ex_adae %>%   mutate(     fl1 = TRUE %>% with_label(\"Total AEs\"),     fl2 = (TRTEMFL == \"Y\") %>%       with_label(\"Total number of patients with at least one adverse event\"),     fl3 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\") %>%       with_label(\"Total number of patients with fatal AEs\"),     fl4 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\" & AEREL == \"Y\") %>%       with_label(\"Total number of patients with related fatal AEs\")   )  # `count_patients_with_flags()`  lyt2 <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_patients_with_flags(     \"SUBJID\",     flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),     denom = \"N_col\"   )  build_table(lyt2, adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                  59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with at least one adverse event   59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with fatal AEs                    28 (40.6%)   31 (42.5%)     20 (34.5%)   #> Total number of patients with related fatal AEs            28 (40.6%)   31 (42.5%)     20 (34.5%)    # `s_count_patients_with_flags()`  s_count_patients_with_flags(   adae,   \"SUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),   denom = \"N_col\",   .N_col = 1000 ) #> $n #> $n$`Total AEs` #> [1] 164 #>  #> $n$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $n$`Total number of patients with fatal AEs` #> [1] 164 #>  #> $n$`Total number of patients with related fatal AEs` #> [1] 164 #>  #>  #> $count #> $count$`Total AEs` #> [1] 164 #>  #> $count$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $count$`Total number of patients with fatal AEs` #> [1] 79 #>  #> $count$`Total number of patients with related fatal AEs` #> [1] 79 #>  #>  #> $count_fraction #> $count_fraction$`Total AEs` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with at least one adverse event` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with fatal AEs` #> [1] 79.000  0.079 #>  #> $count_fraction$`Total number of patients with related fatal AEs` #> [1] 79.000  0.079 #>  #>  #> $n_blq #> $n_blq$`Total AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with at least one adverse event` #> [1] 0 #>  #> $n_blq$`Total number of patients with fatal AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with related fatal AEs` #> [1] 0 #>  #>   #  We need to ungroup `count_fraction` first so that the `rtables` formatting # function `format_count_fraction()` can be applied correctly.  # `a_count_patients_with_flags()`  afun <- make_afun(a_count_patients_with_flags,   .stats = \"count_fraction\",   .ungroup_stats = \"count_fraction\" ) afun(   adae,   .N_col = 10L,   .N_row = 10L,   .var = \"USUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\") ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                                                   row_name formatted_cell #> 1                                                Total AEs     164 (100%) #> 2 Total number of patients with at least one adverse event     164 (100%) #> 3                  Total number of patients with fatal AEs     79 (48.2%) #> 4          Total number of patients with related fatal AEs     79 (48.2%) #>   indent_mod                                                row_label #> 1          0                                                Total AEs #> 2          0 Total number of patients with at least one adverse event #> 3          0                  Total number of patients with fatal AEs #> 4          0          Total number of patients with related fatal AEs"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Count specific values — count_values","title":"Count specific values — count_values","text":"analyze function count_values() creates layout element calculate counts specific values within variable interest. function analyzes one variables interest supplied vector vars. Values count variable(s) vars can given vector via values argument. One row counts generated variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count specific values — count_values","text":"","code":"count_values(   lyt,   vars,   values,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = c(count_fraction = paste(values, collapse = \", \")),   .indent_mods = NULL )  s_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  # S3 method for class 'character' s_count_values(x, values = \"Y\", na.rm = TRUE, ...)  # S3 method for class 'factor' s_count_values(x, values = \"Y\", ...)  # S3 method for class 'logical' s_count_values(x, values = TRUE, ...)  a_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count specific values — count_values","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . values (character) specific values counted. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"count_values\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count specific values — count_values","text":"count_values() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_values() table layout. s_count_values() returns output s_summary() specified values non-numeric variable. a_count_values() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count specific values — count_values","text":"count_values(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_values(): S3 generic function count values. s_count_values(character): Method character class. s_count_values(factor): Method factor class. makes automatic conversion character forwards method characters. s_count_values(logical): Method logical class. a_count_values(): Formatted analysis function used afun count_values().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count specific values — count_values","text":"factor variables, s_count_values checks whether values included levels x fails otherwise. count_values(), variable labels shown one element vars, otherwise hidden.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/count_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count specific values — count_values","text":"","code":"# `count_values` basic_table() %>%   count_values(\"Species\", values = \"setosa\") %>%   build_table(iris) #>            all obs   #> ———————————————————— #> setosa   50 (33.33%)  # `s_count_values.character` s_count_values(x = c(\"a\", \"b\", \"a\"), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>  s_count_values(x = c(\"a\", \"b\", \"a\", NA, NA), values = \"b\", na.rm = FALSE) #> $n #> [1] 5 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.2 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.factor` s_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.logical` s_count_values(x = c(TRUE, FALSE, TRUE)) #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `a_count_values` a_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\", .N_col = 10, .N_row = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n              3          0              n #> 2          count              2          0          count #> 3 count_fraction     2 (66.67%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox proportional hazards regression — cox_regression","title":"Cox proportional hazards regression — cox_regression","text":"Fits Cox regression model estimates hazard ratio describe effect size survival analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox proportional hazards regression — cox_regression","text":"","code":"summarize_coxreg(   lyt,   variables,   control = control_coxreg(),   at = list(),   multivar = FALSE,   common_var = \"STUDYID\",   .stats = c(\"n\", \"hr\", \"ci\", \"pval\", \"pval_inter\"),   .formats = c(n = \"xx\", hr = \"xx.xx\", ci = \"(xx.xx, xx.xx)\", pval =     \"x.xxxx | (<0.0001)\", pval_inter = \"x.xxxx | (<0.0001)\"),   varlabels = NULL,   .indent_mods = NULL,   na_str = \"\",   .section_div = NA_character_ )  s_coxreg(model_df, .stats, .which_vars = \"all\", .var_nms = NULL)  a_coxreg(   df,   labelstr,   eff = FALSE,   var_main = FALSE,   multivar = FALSE,   variables,   at = list(),   control = control_coxreg(),   .spl_context,   .stats,   .formats,   .indent_mods = NULL,   na_str = \"\",   cache_env = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox proportional hazards regression — cox_regression","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. control (list) list parameters returned helper function control_coxreg(). (list numeric) candidate covariate numeric, use specify value covariate effect estimated. multivar (flag) whether multivariate Cox regression run (defaults FALSE), otherwise univariate Cox regression run. common_var (string) name factor variable dataset takes value rows. created pre-processing variable currently exists. .stats (character) names statistics reported among: n: number observations (univariate ) hr: hazard ratio ci: confidence interval pval: p-value treatment effect pval_inter: p-value interaction effect treatment covariate (univariate ) .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. varlabels (list) named list corresponds names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) custom string replace NA values . Defaults \"\". .section_div (string NA) string repeated section divider sections. Defaults NA section divider. vector two strings given, first used treatment covariate sections second different covariates. model_df (data.frame) contains resulting model fit fit_coxreg function tidying applied via broom::tidy(). .which_vars (character) rows statistics returned given model. Defaults \"\". options include \"var_main\" main effects, \"inter\" interaction effects, \"multi_lvl\" multivariate model covariate level rows. .which_vars \"\", specific variables can selected specifying .var_nms. .var_nms (character) term value rows df .stats returned. Typically name variable. using variable labels, var vector desired variable name variable label order see .stats related variable. .which_vars \"var_main\", .var_nms variable name. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. eff (flag) whether treatment effect calculated. Defaults FALSE. var_main (flag) whether main effects calculated. Defaults FALSE. .spl_context (data.frame) gives information ancestor split states passed rtables. cache_env (environment) environment object used cache regression model order avoid repeatedly fitting model every row table. Defaults NULL (caching).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add Cox regression table containing chosen statistics table layout. s_coxreg() returns selected statistic Cox regression model selected variable(s). a_coxreg() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox proportional hazards regression — cox_regression","text":"Cox models commonly used methods estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis (NEST Team, 2020).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg(): Layout-creating function creates Cox regression summary table layout. function wrapper several rtables layouting functions. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). s_coxreg(): Statistics function transforms results tabulated fit_coxreg_univar() fit_coxreg_multivar() list. a_coxreg(): Analysis function used afun rtables::analyze() cfun rtables::summarize_row_groups() within summarize_coxreg().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox proportional hazards regression — cox_regression","text":"","code":"library(survival)  # Testing dataset [survival::bladder]. set.seed(1, kind = \"Mersenne-Twister\") dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   tibble::tibble(     TIME = stop,     STATUS = event,     ARM = as.factor(rx),     COVAR1 = as.factor(enum) %>% formatters::with_label(\"A Covariate Label\"),     COVAR2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     ) %>% formatters::with_label(\"Sex (F/M)\")   ) ) dta_bladder$AGE <- sample(20:60, size = nrow(dta_bladder), replace = TRUE) dta_bladder$STUDYID <- factor(\"X\")  u1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  u2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  m1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  m2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  # summarize_coxreg  result_univar <- basic_table() %>%   summarize_coxreg(variables = u1_variables) %>%   build_table(dta_bladder) result_univar #>                        n    Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————— #> Treatment:                                                        #>   2 vs control (1)    340       0.64       (0.43, 0.94)   0.0242  #> Covariate:                                                        #>   A Covariate Label   340       0.61       (0.41, 0.90)   0.0126  #>   Sex (F/M)           340       0.62       (0.42, 0.92)   0.0182   result_univar_covs <- basic_table() %>%   summarize_coxreg(     variables = u2_variables,   ) %>%   build_table(dta_bladder) result_univar_covs #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.45       (0.28, 0.71)   0.0007  #>     3                                     0.31       (0.19, 0.52)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.33       (0.91, 1.94)   0.1414   result_multivar <- basic_table() %>%   summarize_coxreg(     variables = m1_variables,     multivar = TRUE,   ) %>%   build_table(dta_bladder) result_multivar #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Treatment:                                                                  #>   ARM (reference = 1)                                                       #>     2                                     0.61       (0.41, 0.90)   0.0123  #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.46       (0.28, 0.73)   0.0011  #>     3                                     0.31       (0.18, 0.51)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.29       (0.88, 1.89)   0.1911   result_multivar_covs <- basic_table() %>%   summarize_coxreg(     variables = m2_variables,     multivar = TRUE,     varlabels = c(\"Covariate 1\", \"Covariate 2\") # custom labels   ) %>%   build_table(dta_bladder) result_multivar_covs #>                                 Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————————— #> Covariate:                                                            #>   Covariate 1 (reference = 1)                                 <0.0001 #>     2                               0.46       (0.29, 0.74)   0.0012  #>     3                               0.31       (0.19, 0.52)   <0.0001 #>     4                               0.19       (0.10, 0.34)   <0.0001 #>   Covariate 2 (reference = F)                                         #>     M                               1.29       (0.88, 1.88)   0.1958   # s_coxreg  # Univariate univar_model <- fit_coxreg_univar(variables = u1_variables, data = dta_bladder) df1 <- broom::tidy(univar_model)  s_coxreg(model_df = df1, .stats = \"hr\") #> $hr #> $hr$`2 vs control (1)` #> [1] 0.6386426 #>  #>  #> $hr #> $hr$`A Covariate Label` #> [1] 0.607037 #>  #>  #> $hr #> $hr$`Sex (F/M)` #> [1] 0.6242738 #>  #>   # Univariate with interactions univar_model_inter <- fit_coxreg_univar(   variables = u1_variables, control = control_coxreg(interaction = TRUE), data = dta_bladder ) df1_inter <- broom::tidy(univar_model_inter)  s_coxreg(model_df = df1_inter, .stats = \"hr\", .which_vars = \"inter\", .var_nms = \"COVAR1\") #> $hr #> $hr$`  1` #> [1] 0.6284569 #>  #> $hr$`  2` #> [1] 0.5806499 #>  #> $hr$`  3` #> [1] 0.5486103 #>  #> $hr$`  4` #> [1] 0.6910725 #>  #>   # Univariate without treatment arm - only \"COVAR2\" covariate effects univar_covs_model <- fit_coxreg_univar(variables = u2_variables, data = dta_bladder) df1_covs <- broom::tidy(univar_covs_model)  s_coxreg(model_df = df1_covs, .stats = \"hr\", .var_nms = c(\"COVAR2\", \"Sex (F/M)\")) #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.3271 #>  #>   # Multivariate. multivar_model <- fit_coxreg_multivar(variables = m1_variables, data = dta_bladder) df2 <- broom::tidy(multivar_model)  s_coxreg(model_df = df2, .stats = \"pval\", .which_vars = \"var_main\", .var_nms = \"COVAR1\") #> $pval #> $pval$`A Covariate Label (reference = 1)` #> [1] 7.209956e-09 #>  #>  s_coxreg(   model_df = df2, .stats = \"pval\", .which_vars = \"multi_lvl\",   .var_nms = c(\"COVAR1\", \"A Covariate Label\") ) #> $pval #> $pval$`2` #> [1] 0.001120332 #>  #> $pval$`3` #> [1] 6.293725e-06 #>  #> $pval$`4` #> [1] 3.013875e-08 #>  #>   # Multivariate without treatment arm - only \"COVAR1\" main effect multivar_covs_model <- fit_coxreg_multivar(variables = m2_variables, data = dta_bladder) df2_covs <- broom::tidy(multivar_covs_model)  s_coxreg(model_df = df2_covs, .stats = \"hr\") #> $hr #> $hr$`2` #> [1] 0.4600728 #>  #> $hr$`3` #> [1] 0.3100455 #>  #> $hr$`4` #> [1] 0.1854177 #>  #>  #> $hr #> $hr$`A Covariate Label (reference = 1)` #> numeric(0) #>  #>  #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.285406 #>  #>   a_coxreg(   df = dta_bladder,   labelstr = \"Label 1\",   variables = u1_variables,   .spl_context = list(value = \"COVAR1\"),   .stats = \"n\",   .formats = \"xx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1  Label 1            340          0   Label 1  a_coxreg(   df = dta_bladder,   labelstr = \"\",   variables = u1_variables,   .spl_context = list(value = \"COVAR2\"),   .stats = \"pval\",   .formats = \"xx.xxxx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1 Sex (F/M)         0.0182          0 Sex (F/M)"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox regression helper function for interactions — cox_regression_inter","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Test estimate effect treatment interaction covariate. effect estimated HR tested treatment given level covariate, comparison treatment control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"h_coxreg_inter_effect(x, effect, covar, mod, label, control, ...)  # S3 method for class 'numeric' h_coxreg_inter_effect(x, effect, covar, mod, label, control, at, ...)  # S3 method for class 'factor' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  # S3 method for class 'character' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  h_coxreg_extract_interaction(effect, covar, mod, data, at, control)  h_coxreg_inter_estimations(   variable,   given,   lvl_var,   lvl_given,   mod,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox regression helper function for interactions — cox_regression_inter","text":"x (numeric factor) values covariate tested. effect (string) name effect tested estimated. covar (string) name covariate model. mod (coxph) fitted Cox regression model (see survival::coxph()). label (string) label returned term_label. control (list) list controls returned control_coxreg(). ... see methods. (list) list items named covariate, every item vector levels interaction estimated. data (data.frame) data frame model fit. variable, given (string) name variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect() returns data.frame covariate interaction effects consisting following variables: effect, term, term_label, level, n, hr, lcl, ucl, pval, pval_inter. h_coxreg_extract_interaction() returns result interaction test estimated values. interaction, h_coxreg_univar_extract() applied instead. h_coxreg_inter_estimations() returns list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female) model abbreviated: y ~ Arm + Sex + Arm:Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) estimation Hazard Ratio arm C/sex M given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5). interaction coefficient deduced b2 + b5 standard error obtained $sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect(): S3 generic helper function determine interaction effect. h_coxreg_inter_effect(numeric): Method numeric class. Estimates interaction numeric covariate. h_coxreg_inter_effect(factor): Method factor class. Estimate interaction factor covariate. h_coxreg_inter_effect(character): Method character class. Estimate interaction character covariate. makes automatic conversion factor forwards method factors. h_coxreg_extract_interaction(): higher level function get results interaction test estimated values. h_coxreg_inter_estimations(): Hazard ratio estimation interactions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Automatic conversion character factor guarantee results can generated correctly. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cox_regression_inter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4,       labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) h_coxreg_extract_interaction(   mod = mod, effect = \"armcd\", covar = \"covar1\", data = dta_bladder,   control = control_coxreg() ) #>                    effect   term        term_label level   n        hr #> 1              Covariate: covar1 A Covariate Label       340        NA #> armcd2/covar11 Covariate: covar1                 1     1  NA 0.6341111 #> armcd2/covar12 Covariate: covar1                 2     2  NA 0.5845305 #> armcd2/covar13 Covariate: covar1                 3     3  NA 0.5507703 #> armcd2/covar14 Covariate: covar1                 4     4  NA 0.6910643 #>                      lcl      ucl      pval pval_inter #> 1                     NA       NA 0.1302825   0.988245 #> armcd2/covar11 0.3514676 1.144051        NA         NA #> armcd2/covar12 0.2716689 1.257692        NA         NA #> armcd2/covar13 0.2244668 1.351415        NA         NA #> armcd2/covar14 0.2315248 2.062715        NA         NA  mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) result <- h_coxreg_inter_estimations(   variable = \"armcd\", given = \"covar1\",   lvl_var = levels(dta_bladder$armcd),   lvl_given = levels(dta_bladder$covar1),   mod = mod, conf_level = .95 ) result #> $armcd2 #>                      coef  se(coef)        hr       lcl      ucl #> armcd2/covar11 -0.4555312 0.3010803 0.6341111 0.3514676 1.144051 #> armcd2/covar12 -0.5369464 0.3909383 0.5845305 0.2716689 1.257692 #> armcd2/covar13 -0.5964375 0.4579624 0.5507703 0.2244668 1.351415 #> armcd2/covar14 -0.3695225 0.5579418 0.6910643 0.2315248 2.062715 #>  #> attr(,\"details\") #> [1] \"Estimations of armcd hazard ratio given the level of covar1 compared to armcd level 1.\""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":null,"dir":"Reference","previous_headings":"","what":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"cuts numeric vector sample quantile bins.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"cut_quantile_bins(   x,   probs = c(0.25, 0.5, 0.75),   labels = NULL,   type = 7,   ordered = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"x (numeric) continuous variable values cut quantile bins. may contain NA values, used quantile calculations, included return vector. probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. labels (character) unique labels quantile bins. n probabilities probs, must n + 1 long. type (integer(1)) type quantiles use, see stats::quantile() details. ordered (flag) result ordered factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"factor variable appropriately-labeled bins levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"Intervals closed right side. , first bin interval [-Inf, q1] q1 first quantile, second bin (q1, q2], etc., last bin (qn, +Inf] qn last quantile.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/cut_quantile_bins.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"# Default is to cut into quartile bins. cut_quantile_bins(cars$speed) #>  [1] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #>  [7] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #> [13] [0%,25%]   [0%,25%]   [0%,25%]   (25%,50%]  (25%,50%]  (25%,50%]  #> [19] (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [25] (25%,50%]  (25%,50%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [31] (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [37] (50%,75%]  (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [43] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [49] (75%,100%] (75%,100%] #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%]  # Use custom quantiles. cut_quantile_bins(cars$speed, probs = c(0.1, 0.2, 0.6, 0.88)) #>  [1] [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   (10%,20%]  #>  [7] (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (20%,60%]  #> [13] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [19] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [25] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [31] (20%,60%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [37] (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [43] (60%,88%]  (60%,88%]  (88%,100%] (88%,100%] (88%,100%] (88%,100%] #> [49] (88%,100%] (88%,100%] #> Levels: [0%,10%] < (10%,20%] < (20%,60%] < (60%,88%] < (88%,100%]  # Use custom labels. cut_quantile_bins(cars$speed, labels = paste0(\"Q\", 1:4)) #>  [1] Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 #> [26] Q2 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 #> Levels: Q1 < Q2 < Q3 < Q4  # NAs are preserved in result factor. ozone_binned <- cut_quantile_bins(airquality$Ozone) which(is.na(ozone_binned)) #>  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54 #> [20]  55  56  57  58  59  60  61  65  72  75  83  84 102 103 107 115 119 150 # So you might want to make these explicit. explicit_na(ozone_binned) #>   [1] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   <Missing>  (25%,50%]  #>   [7] (25%,50%]  (25%,50%]  [0%,25%]   <Missing>  [0%,25%]   [0%,25%]   #>  [13] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  [0%,25%]   #>  [19] (25%,50%]  [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  #>  [25] <Missing>  <Missing>  <Missing>  (25%,50%]  (50%,75%]  (75%,100%] #>  [31] (50%,75%]  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [37] <Missing>  (25%,50%]  <Missing>  (75%,100%] (50%,75%]  <Missing>  #>  [43] <Missing>  (25%,50%]  <Missing>  <Missing>  (25%,50%]  (50%,75%]  #>  [49] (25%,50%]  [0%,25%]   [0%,25%]   <Missing>  <Missing>  <Missing>  #>  [55] <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [61] <Missing>  (75%,100%] (50%,75%]  (50%,75%]  <Missing>  (75%,100%] #>  [67] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #>  [73] [0%,25%]   (25%,50%]  <Missing>  [0%,25%]   (50%,75%]  (50%,75%]  #>  [79] (50%,75%]  (75%,100%] (50%,75%]  [0%,25%]   <Missing>  <Missing>  #>  [85] (75%,100%] (75%,100%] (25%,50%]  (50%,75%]  (75%,100%] (50%,75%]  #>  [91] (75%,100%] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   (75%,100%] #>  [97] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #> [103] <Missing>  (50%,75%]  (25%,50%]  (75%,100%] <Missing>  (25%,50%]  #> [109] (50%,75%]  (25%,50%]  (25%,50%]  (50%,75%]  (25%,50%]  [0%,25%]   #> [115] <Missing>  (50%,75%]  (75%,100%] (75%,100%] <Missing>  (75%,100%] #> [121] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [127] (75%,100%] (50%,75%]  (50%,75%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [133] (25%,50%]  (50%,75%]  (25%,50%]  (25%,50%]  [0%,25%]   [0%,25%]   #> [139] (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  [0%,25%]   [0%,25%]   #> [145] (25%,50%]  (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  <Missing>  #> [151] [0%,25%]   [0%,25%]   (25%,50%]  #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%] < <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Description function produces labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(abnormal)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"abnormal (character) values identifying abnormal range level(s) .var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Abnormal category labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(\"LOW\") #> $not_abnormal #> [1] \"Not low\" #>  #> $abnormal #> [1] \"Low\" #>  #> $total #> [1] \"Total\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of cumulative count — d_count_cumulative","title":"Description of cumulative count — d_count_cumulative","text":"helper function describes analysis s_count_cumulative().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of cumulative count — d_count_cumulative","text":"","code":"d_count_cumulative(threshold, lower_tail = TRUE, include_eq = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of cumulative count — d_count_cumulative","text":"threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of cumulative count — d_count_cumulative","text":"Labels s_count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"","code":"d_count_missed_doses(thresholds)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"thresholds (numeric) minimum number missed doses patients .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"d_count_missed_doses() returns named character vector labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of standard oncology response — d_onco_rsp_label","title":"Description of standard oncology response — d_onco_rsp_label","text":"Describe oncology response standard way.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of standard oncology response — d_onco_rsp_label","text":"x (character) standard oncology codes described.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of standard oncology response — d_onco_rsp_label","text":"Response labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_onco_rsp_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(   c(\"CR\", \"PR\", \"SD\", \"NON CR/PD\", \"PD\", \"NE\", \"Missing\", \"<Missing>\", \"NE/Missing\") ) #>                           CR                           PR  #>       Complete Response (CR)        Partial Response (PR)  #>                           SD                    NON CR/PD  #>          Stable Disease (SD) Non-CR or Non-PD (NON CR/PD)  #>                           PD                           NE  #>     Progressive Disease (PD)           Not Evaluable (NE)  #>                      Missing                    <Missing>  #>                      Missing                    <Missing>  #>                   NE/Missing  #>       Missing or unevaluable  #> 9 Levels: Complete Response (CR) Partial Response (PR) ... <Missing>  # Adding some values not considered in d_onco_rsp_label  d_onco_rsp_label(   c(\"CR\", \"PR\", \"hello\", \"hi\") ) #>                     CR                     PR                  hello  #> Complete Response (CR)  Partial Response (PR)                  hello  #>                     hi  #>                     hi  #> Levels: Complete Response (CR) Partial Response (PR) hello hi"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate PK reference dataset — d_pkparam","text":"","code":"d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate PK reference dataset — d_pkparam","text":"data.frame PK parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_pkparam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate PK reference dataset — d_pkparam","text":"","code":"pk_reference_dataset <- d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the proportion summary — d_proportion","title":"Description of the proportion summary — d_proportion","text":"helper function describes analysis s_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the proportion summary — d_proportion","text":"","code":"d_proportion(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the proportion summary — d_proportion","text":"conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. long (flag) whether long short (default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the proportion summary — d_proportion","text":"String describing analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of method used for proportion comparison — d_proportion_diff","title":"Description of method used for proportion comparison — d_proportion_diff","text":"auxiliary function describes analysis s_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of method used for proportion comparison — d_proportion_diff","text":"","code":"d_proportion_diff(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of method used for proportion comparison — d_proportion_diff","text":"conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. long (flag) whether long (TRUE) short (FALSE, default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of method used for proportion comparison — d_proportion_diff","text":"string describing analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"Internal function check variables included tabulate_rsp_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"","code":"d_rsp_subgroups_colvars(vars, conf_level = NULL, method = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_rsp_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"list variables tabulate labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"Internal function check variables included tabulate_survival_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"","code":"d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. conf_level (proportion) confidence level interval. method (string) p-value method testing hazard ratio = 1. time_unit (string) label unit median survival time. Default NULL skips displaying unit.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"list variables labels tabulate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_survival_subgroups_colvars.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"least one n_tot n_tot_events must provided vars.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the difference test between two proportions — d_test_proportion_diff","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"auxiliary function describes analysis s_test_proportion_diff.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"","code":"d_test_proportion_diff(method)"},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/d_test_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"string describing test p-value derived.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of days to months — day2month","title":"Conversion of days to months — day2month","text":"Conversion days months","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of days to months — day2month","text":"","code":"day2month(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of days to months — day2month","text":"x (numeric(1)) time days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of days to months — day2month","text":"numeric vector time months.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/day2month.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of days to months — day2month","text":"","code":"x <- c(403, 248, 30, 86) day2month(x) #> [1] 13.2402464  8.1478439  0.9856263  2.8254620"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"function useful label grid grobs (also ggplot2, lattice plots) title, footnote, page numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"decorate_grob(   grob,   titles,   footnotes,   page = \"\",   width_titles = grid::unit(1, \"npc\"),   width_footnotes = grid::unit(1, \"npc\"),   border = TRUE,   padding = grid::unit(rep(1, 4), \"lines\"),   margins = grid::unit(c(1, 0, 1, 0), \"lines\"),   outer_margins = grid::unit(c(2, 1.5, 3, 1.5), \"cm\"),   gp_titles = grid::gpar(),   gp_footnotes = grid::gpar(fontsize = 8),   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grob (grob) grid grob object, optionally NULL grob decoration shown. titles (character) titles given vector strings separated newline wrapped according page width. footnotes (character) footnotes. Uses formatting rules titles. page (string NULL) page numeration. NULL page number displayed. width_titles (grid::unit) width titles. Usually defined available space grid::unit(1, \"npc\"), affected parameter outer_margins. Right margins (outer_margins[4]) need subtracted allowed width. width_footnotes (grid::unit) width footnotes. default margin correction width_titles. border (flag) whether border drawn around plot . padding (grid::unit) padding. unit object length 4. Innermost margin plot (grob) , possibly, border plot. Usually expressed 4 identical values (usually \"lines\"). defaults grid::unit(rep(1, 4), \"lines\"). margins (grid::unit) margins. unit object length 4. Margins plot elements list (e.g. titles, plot, footers). usually expressed 4 \"lines\", lateral ones 0s, top bottom 1s. defaults grid::unit(c(1, 0, 1, 0), \"lines\"). outer_margins (grid::unit) outer margins. unit object length 4. defines general margin plot, considering also decorations like titles, footnotes, page numbers. defaults grid::unit(c(2, 1.5, 3, 1.5), \"cm\"). gp_titles (gpar) gpar object. Mainly used set different \"fontsize\". gp_footnotes (gpar) gpar object. Mainly used set different \"fontsize\". name character identifier grob.  Used find     grob display list /child another grob. gp \"gpar\" object, typically output     call function gpar.  basically     list graphical parameter settings. vp viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grid grob (gTree).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"titles footnotes ragged, .e. title wrapped individually.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"library(grid)  titles <- c(   \"Edgar Anderson's Iris Data\",   paste(     \"This famous (Fisher's or Anderson's) iris data set gives the measurements\",     \"in centimeters of the variables sepal length and width and petal length\",     \"and width, respectively, for 50 flowers from each of 3 species of iris.\"   ) )  footnotes <- c(   \"The species are Iris setosa, versicolor, and virginica.\",   paste(     \"iris is a data frame with 150 cases (rows) and 5 variables (columns) named\",     \"Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, and Species.\"   ) )  ## empty plot grid.newpage()  grid.draw(   decorate_grob(     NULL,     titles = titles,     footnotes = footnotes,     page = \"Page 4 of 10\"   ) )   # grid p <- gTree(   children = gList(     rectGrob(),     xaxisGrob(),     yaxisGrob(),     textGrob(\"Sepal.Length\", y = unit(-4, \"lines\")),     textGrob(\"Petal.Length\", x = unit(-3.5, \"lines\"), rot = 90),     pointsGrob(iris$Sepal.Length, iris$Petal.Length, gp = gpar(col = iris$Species), pch = 16)   ),   vp = vpStack(plotViewport(), dataViewport(xData = iris$Sepal.Length, yData = iris$Petal.Length)) ) grid.newpage() grid.draw(p)   grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with ggplot2 library(ggplot2)  p_gg <- ggplot2::ggplot(iris, aes(Sepal.Length, Sepal.Width, col = Species)) +   ggplot2::geom_point() p_gg  p <- ggplotGrob(p_gg) grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with lattice library(lattice)  xyplot(Sepal.Length ~ Petal.Length, data = iris, col = iris$Species)  p <- grid.grab()  grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   # with gridExtra - no borders library(gridExtra) #>  #> Attaching package: ‘gridExtra’ #> The following object is masked from ‘package:dplyr’: #>  #>     combine grid.newpage() grid.draw(   decorate_grob(     tableGrob(       head(mtcars)     ),     titles = \"title\",     footnotes = \"footnote\",     border = FALSE   ) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Update page number — decorate_grob_factory","title":"Update page number — decorate_grob_factory","text":"Automatically updates page number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update page number — decorate_grob_factory","text":"","code":"decorate_grob_factory(npages, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update page number — decorate_grob_factory","text":"npages (numeric(1)) total number pages. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update page number — decorate_grob_factory","text":"Closure increments page number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Decorate set of grobs and add page numbering — decorate_grob_set","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"Note uses decorate_grob_factory() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"decorate_grob_set(grobs, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"grobs (list grob) list grid grobs. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"decorated grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/decorate_grob_set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"library(ggplot2) library(grid) g <- with(data = iris, {   list(     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Sepal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Petal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     )   ) }) lg <- decorate_grob_set(grobs = g, titles = \"Hello\\nOne\\nTwo\\nThree\", footnotes = \"\")  draw_grob(lg[[1]]) #> Warning: `draw_grob()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  draw_grob(lg[[2]])  draw_grob(lg[[6]])"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string replacement for NA values — default_na_str","title":"Default string replacement for NA values — default_na_str","text":"default string used represent NA values. value used default value na_str argument throughout tern package, printed place NA values output tables. specified tern function user via na_str argument, R environment options via set_default_na_str(), NA used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string replacement for NA values — default_na_str","text":"","code":"default_na_str()  set_default_na_str(na_str)"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string replacement for NA values — default_na_str","text":"na_str (string) single string value set R environment options default value replace NAs. Use getOption(\"tern_default_na_str\") check current value set R environment (defaults NULL set).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string replacement for NA values — default_na_str","text":"default_na_str returns current value R environment option set \"tern_default_na_str\", NA_character_ otherwise. set_default_na_str return value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string replacement for NA values — default_na_str","text":"default_na_str(): Accessor default NA value replacement string. set_default_na_str(): Setter default NA value replacement string. Sets option \"tern_default_na_str\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_na_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string replacement for NA values — default_na_str","text":"","code":"# Default settings default_na_str() #> [1] NA getOption(\"tern_default_na_str\") #> NULL  # Set custom value set_default_na_str(\"<Missing>\")  # Settings after value has been set default_na_str() #> [1] \"<Missing>\" getOption(\"tern_default_na_str\") #> [1] \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Utility functions get valid statistic methods different method groups (.stats) associated formats (.formats), labels (.labels), indent modifiers (.indent_mods). utility used across tern, working principles can seen analyze_vars(). See notes understand experimental.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"get_stats(   method_groups = \"analyze_vars_numeric\",   stats_in = NULL,   add_pval = FALSE )  get_formats_from_stats(stats, formats_in = NULL)  get_labels_from_stats(stats, labels_in = NULL, row_nms = NULL)  get_indents_from_stats(stats, indents_in = NULL, row_nms = NULL)  tern_default_stats  tern_default_formats  tern_default_labels  summary_formats(type = \"numeric\", include_pval = FALSE)  summary_labels(type = \"numeric\", include_pval = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"tern_default_stats named list available statistics, element named corresponding statistical method group. tern_default_formats named vector available default formats, element named corresponding statistic. tern_default_labels named character vector available default labels, element named corresponding statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"method_groups (character) indicates statistical method group (tern analyze function) retrieve default statistics . character vector can used specify one statistical method group. stats_in (character) statistics retrieve selected method group. add_pval (flag) \"pval\" (\"pval_counts\" method_groups contains \"analyze_vars_counts\") added statistical methods? stats (character) statistical methods get defaults . formats_in (named vector) inserted formats replace defaults. can character vector formatters::list_valid_format_labels() custom format function. labels_in (named character) inserted labels replace defaults. row_nms (character) row names. Levels factor character variable, statistics .stats calculated . parameter set, variable levels used defaults, names given custom values correspond levels (format statistic.level) instead statistics. Can also variable names rows correspond different variables instead levels. Defaults NULL. indents_in (named vector) inserted indent modifiers replace defaults (default 0L). type (string)\"numeric\" \"counts\". include_pval (flag) add_pval argument get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats() returns character vector statistical methods. get_formats_from_stats() returns named vector formats (present either tern_default_formats formats_in, otherwise NULL). Values can taken formatters::list_valid_format_labels() custom function (e.g. formatting_functions). get_labels_from_stats() returns named character vector labels (present either tern_default_labels labels_in, otherwise NULL). get_indents_from_stats() returns single indent modifier value apply rows named numeric vector indent modifiers (present, otherwise NULL). summary_formats() returns named vector default statistic formats given data type. summary_labels returns named vector default statistic labels given data type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Current choices type counts numeric analyze_vars() affect get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats(): Get statistics available given method group (analyze function). check available defaults see tern::tern_default_stats list. get_formats_from_stats(): Get formats corresponding list statistics. check available defaults see tern::tern_default_formats list. get_labels_from_stats(): Get labels corresponding list statistics. check available defaults see tern::tern_default_labels list. available , statistics name used label. get_indents_from_stats(): Format indent modifiers given vector/list statistics. defaults 0L values. tern_default_stats: Named list available statistics method group tern. tern_default_formats: Named vector default formats tern. tern_default_labels: Named character vector default labels tern. summary_formats():  Quick function retrieve default formats summary statistics: analyze_vars() analyze_vars_in_cols() principally. summary_labels():  Quick function retrieve default labels summary statistics. Returns labels descriptive statistics understood rtables. Similar summary_formats.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"defaults experimental use names functions retrieve default statistics. generalized groups methods according reasonable groupings. Formats tern rtables can functions take table cell value return string. well documented vignette(\"custom_appearance\", package = \"rtables\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/default_stats_formats_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"# analyze_vars is numeric num_stats <- get_stats(\"analyze_vars_numeric\") # also the default  # Other type cnt_stats <- get_stats(\"analyze_vars_counts\")  # Weirdly taking the pval from count_occurrences only_pval <- get_stats(\"count_occurrences\", add_pval = TRUE, stats_in = \"pval\")  # All count_occurrences all_cnt_occ <- get_stats(\"count_occurrences\")  # Multiple get_stats(c(\"count_occurrences\", \"analyze_vars_counts\")) #> [1] \"count\"                   \"count_fraction\"          #> [3] \"count_fraction_fixed_dp\" \"fraction\"                #> [5] \"n\"                       \"n_blq\"                    # Defaults formats get_formats_from_stats(num_stats) #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  get_formats_from_stats(cnt_stats) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  get_formats_from_stats(only_pval) #> $pval #> [1] \"x.xxxx | (<0.0001)\" #>  get_formats_from_stats(all_cnt_occ) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>   # Addition of customs get_formats_from_stats(all_cnt_occ, formats_in = c(\"fraction\" = c(\"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx\" #>  get_formats_from_stats(all_cnt_occ, formats_in = list(\"fraction\" = c(\"xx.xx\", \"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx.xx\" \"xx\"    #>   # Defaults labels get_labels_from_stats(num_stats) #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  get_labels_from_stats(cnt_stats) #>                       n                   count          count_fraction  #>                     \"n\"                 \"count\"        \"count_fraction\"  #> count_fraction_fixed_dp                fraction                   n_blq  #>        \"count_fraction\"              \"fraction\"                 \"n_blq\"  get_labels_from_stats(only_pval) #>               pval  #> \"p-value (t-test)\"  get_labels_from_stats(all_cnt_occ) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"fraction\"   # Addition of customs get_labels_from_stats(all_cnt_occ, labels_in = c(\"fraction\" = \"Fraction\")) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"Fraction\"  get_labels_from_stats(all_cnt_occ, labels_in = list(\"fraction\" = c(\"Some more fractions\"))) #> $count #> [1] \"count\" #>  #> $count_fraction #> [1] \"count_fraction\" #>  #> $count_fraction_fixed_dp #> [1] \"count_fraction\" #>  #> $fraction #> [1] \"Some more fractions\" #>   get_indents_from_stats(all_cnt_occ, indents_in = 3L) #> [1] 3 3 3 3 get_indents_from_stats(all_cnt_occ, indents_in = list(count = 2L, count_fraction = 5L)) #> $count #> [1] 2 #>  #> $count_fraction #> [1] 5 #>  #> $count_fraction_fixed_dp #> [1] 0 #>  #> $fraction #> [1] 0 #>  get_indents_from_stats(   all_cnt_occ,   indents_in = list(a = 2L, count.a = 1L, count.b = 5L), row_nms = c(\"a\", \"b\") ) #> $count.a #> [1] 1 #>  #> $count.b #> [1] 5 #>  #> $count_fraction.a #> [1] 2 #>  #> $count_fraction.b #> [1] 0 #>  #> $count_fraction_fixed_dp.a #> [1] 2 #>  #> $count_fraction_fixed_dp.b #> [1] 0 #>  #> $fraction.a #> [1] 2 #>  #> $fraction.b #> [1] 0 #>   summary_formats() #> Warning: `summary_formats()` was deprecated in tern 0.9.6. #> ℹ Use get_formats_from_stats(get_stats(\"analyze_vars_numeric\", add_pval = #>   include_pval)) instead #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  summary_formats(type = \"counts\", include_pval = TRUE) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  #> $pval_counts #> [1] \"x.xxxx | (<0.0001)\" #>   summary_labels() #> Warning: `summary_formats()` was deprecated in tern 0.9.6. #> ℹ Use get_labels_from_stats(get_stats(\"analyze_vars_numeric\", add_pval = #>   include_pval)) instead #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  summary_labels(type = \"counts\", include_pval = TRUE) #>                            n                        count  #>                          \"n\"                      \"count\"  #>               count_fraction      count_fraction_fixed_dp  #>             \"count_fraction\"             \"count_fraction\"  #>                     fraction                        n_blq  #>                   \"fraction\"                      \"n_blq\"  #>                  pval_counts  #> \"p-value (chi-squared test)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for a difference of binomials — desctools_binom","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"Several confidence intervals difference proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"","code":"desctools_binom(   x1,   n1,   x2,   n2,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"ac\", \"wald\", \"waldcc\", \"score\", \"scorecc\", \"mn\", \"mee\", \"blj\", \"ha\", \"hal\",     \"jp\") )  desctools_binomci(   x,   n,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"wilson\", \"wald\", \"waldcc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\",     \"wilsoncc\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\",     \"pratt\", \"midp\", \"lik\", \"blaker\"),   rand = 123,   tol = 1e-05 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"conf.level (proportion) confidence level, defaults 0.95. sides (string) side confidence interval compute. Must one \"two-sided\" (default), \"left\", \"right\". method (string) method use. Can one : \"wald\", \"wilson\", \"wilsoncc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\", \"pratt\", \"midp\", \"lik\", \"blaker\". x (integer(1)) number successes. n (integer(1)) number trials.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"matrix 3 values: est: estimate proportion difference. lwr.ci: estimate lower end confidence interval. upr.ci: estimate upper end confidence interval. matrix 3 columns containing: est: estimate proportion difference. lwr.ci: lower end confidence interval. upr.ci: upper end confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/desctools_binom.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"desctools_binom(): Several confidence intervals difference proportions. desctools_binomci(): Compute confidence intervals binomial proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.frame object to ggplot object — df2gg","title":"Convert data.frame object to ggplot object — df2gg","text":"Given data.frame object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"df2gg(   df,   colwidths = NULL,   font_size = 10,   col_labels = TRUE,   col_lab_fontface = \"bold\",   hline = TRUE,   bg_fill = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.frame object to ggplot object — df2gg","text":"df (data.frame) data frame. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column df position. NULL, column widths calculated according maximum number characters per column. font_size (numeric(1)) font size. col_labels (flag) whether column names (labels) df used first row output table. col_lab_fontface (string) font face apply first row (column labels col_labels = TRUE). Defaults \"bold\". hline (flag) whether horizontal line printed first row table. bg_fill (string) table background fill color.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.frame object to ggplot object — df2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"if (FALSE) { # \\dontrun{ df2gg(head(iris, 5))  df2gg(head(iris, 5), font_size = 15, colwidths = c(1, 1, 1, 1, 1)) } # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Encode categorical missing values in a data frame — df_explicit_na","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"helper function encode missing entries across groups categorical variables data frame.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"df_explicit_na(   data,   omit_columns = NULL,   char_as_factor = TRUE,   logical_as_factor = FALSE,   na_level = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data (data.frame) data set. omit_columns (character) names variables data modified function. char_as_factor (flag) whether convert character variables data factors. logical_as_factor (flag) whether convert logical variables data factors. na_level (string) string used replace NA empty values inside non-omit_columns columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data.frame chosen modifications applied.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"Missing entries NA empty strings replaced specified value. factor variables include missing values, missing value inserted last level. Similarly, case character logical variables converted factors char_as_factor logical_as_factor options, missing values set last level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/df_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"my_data <- data.frame(   u = c(TRUE, FALSE, NA, TRUE),   v = factor(c(\"A\", NA, NA, NA), levels = c(\"Z\", \"A\")),   w = c(\"A\", \"B\", NA, \"C\"),   x = c(\"D\", \"E\", \"F\", NA),   y = c(\"G\", \"H\", \"I\", \"\"),   z = c(1, 2, 3, 4),   stringsAsFactors = FALSE )  # Example 1 # Encode missing values in all character or factor columns. df_explicit_na(my_data) #>       u         v         w         x         y z #> 1  TRUE         A         A         D         G 1 #> 2 FALSE <Missing>         B         E         H 2 #> 3    NA <Missing> <Missing>         F         I 3 #> 4  TRUE <Missing>         C <Missing> <Missing> 4 # Also convert logical columns to factor columns. df_explicit_na(my_data, logical_as_factor = TRUE) #>           u         v         w         x         y z #> 1      TRUE         A         A         D         G 1 #> 2     FALSE <Missing>         B         E         H 2 #> 3 <Missing> <Missing> <Missing>         F         I 3 #> 4      TRUE <Missing>         C <Missing> <Missing> 4 # Encode missing values in a subset of columns. df_explicit_na(my_data, omit_columns = c(\"x\", \"y\")) #>       u         v         w    x y z #> 1  TRUE         A         A    D G 1 #> 2 FALSE <Missing>         B    E H 2 #> 3    NA <Missing> <Missing>    F I 3 #> 4  TRUE <Missing>         C <NA>   4  # Example 2 # Here we purposefully convert all `M` values to `NA` in the `SEX` variable. # After running `df_explicit_na` the `NA` values are encoded as `<Missing>` but they are not # included when generating `rtables`. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  # If you want the `Na` values to be displayed in the table use the `na_level` argument. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  # Example 3 # Numeric variables that have missing values are not altered. This means that any `NA` value in # a numeric variable will not be included in the summary statistics, nor will they be included # in the denominator value for calculating the percent values. adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)"},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to check if a float value is equal to another float value — .is_equal_float","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"Uses .Machine$double.eps tolerance comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"","code":".is_equal_float(x, y)"},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"x (numeric(1)) float number. y (numeric(1)) float number.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/dot-is_equal_float.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"TRUE identical, otherwise FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw grob — draw_grob","title":"Draw grob — draw_grob","text":"Draw grob device page.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw grob — draw_grob","text":"","code":"draw_grob(grob, newpage = TRUE, vp = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw grob — draw_grob","text":"grob (grob) grid object. newpage (flag) draw new page. vp (viewport NULL) viewport() object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw grob — draw_grob","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/draw_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw grob — draw_grob","text":"","code":"library(dplyr) library(grid)  # \\donttest{ rect <- rectGrob(width = grid::unit(0.5, \"npc\"), height = grid::unit(0.5, \"npc\")) rect %>% draw_grob(vp = grid::viewport(angle = 45))   num <- lapply(1:10, textGrob) num %>%   arrange_grobs(grobs = .) %>%   draw_grob() #> Warning: `stack_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>. showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Return an empty numeric if all elements are NA. — empty_vector_if_na","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"Return empty numeric elements NA.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"empty_vector_if_na(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"x (numeric) vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"empty numeric elements x NA, otherwise x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/empty_vector_if_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"x <- c(NA, NA, NA) # Internal function - empty_vector_if_na"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":null,"dir":"Reference","previous_headings":"","what":"Hazard ratio estimation in interactions — estimate_coef","title":"Hazard ratio estimation in interactions — estimate_coef","text":"function estimates hazard ratios arms interaction variable given specific values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"estimate_coef(   variable,   given,   lvl_var,   lvl_given,   coef,   mmat,   vcov,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hazard ratio estimation in interactions — estimate_coef","text":"variable, given (character(2)) names two variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). coef (numeric) vector estimated coefficients. mmat (named numeric) vector filled 0s used template obtain design matrix. vcov (matrix) variance-covariance matrix underlying model. conf_level (proportion) confidence level estimate intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hazard ratio estimation in interactions — estimate_coef","text":"list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hazard ratio estimation in interactions — estimate_coef","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female). model abbreviated: y ~ Arm + Sex + Arm x Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) Given want estimation Hazard Ratio arm C/sex M, estimation given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5), therefore interaction coefficient given b2 + b5 standard error obtained $1.96 * sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$ confidence level 0.95.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_coef.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"library(dplyr) library(survival)  ADSL <- tern_ex_adsl %>%   filter(SEX %in% c(\"F\", \"M\"))  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"PFS\") adtte$ARMCD <- droplevels(adtte$ARMCD) adtte$SEX <- droplevels(adtte$SEX)  mod <- coxph(   formula = Surv(time = AVAL, event = 1 - CNSR) ~ (SEX + ARMCD)^2,   data = adtte )  mmat <- stats::model.matrix(mod)[1, ] mmat[!mmat == 0] <- 0"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"analyze & summarize function estimate_multinomial_response() creates layout element estimate proportion proportion confidence interval level factor variable. primary analysis variable, var, factor variable, values used labels within output table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"estimate_multinomial_response(   lyt,   var,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = var,   .stats = \"prop_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_length_proportion(x, .N_col, ...)  a_length_proportion(x, .N_col, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"estimate_multinomial_response\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_length_proportion() table layout. s_length_proportion() returns statistics s_proportion(). a_length_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze() rtables::summarize_row_groups(). s_length_proportion(): Statistics function feeds length x number successes, .N_col total number successes failures s_proportion(). a_length_proportion(): Formatted analysis function used afun estimate_multinomial_response().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_multinomial_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"library(dplyr)  # Use of the layout creating function. dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = factor(rep(LETTERS[1:3], each = 4)),   AVAL    = c(A = c(1, 1, 1, 1), B = c(0, 0, 1, 1), C = c(0, 0, 0, 0)) ) %>% mutate(   AVALC = factor(AVAL,     levels = c(0, 1),     labels = c(\"Complete Response (CR)\", \"Partial Response (PR)\")   ) )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_multinomial_response(var = \"AVALC\")  tbl <- build_table(lyt, dta_test)  tbl #>                                           A                B                 C        #> ————————————————————————————————————————————————————————————————————————————————————— #> Complete Response (CR)                0 (0.0%)         2 (50.0%)        4 (100.0%)    #>   95% CI (Wald, with correction)    (0.00, 12.50)    (0.00, 100.00)   (87.50, 100.00) #> Partial Response (PR)                4 (100.0%)        2 (50.0%)         0 (0.0%)     #>   95% CI (Wald, with correction)   (87.50, 100.00)   (0.00, 100.00)    (0.00, 12.50)   s_length_proportion(rep(\"CR\", 10), .N_col = 100) #> $n_prop #> [1] 10.0  0.1 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  3.620108 16.379892 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>  s_length_proportion(factor(character(0)), .N_col = 100) #> $n_prop #> [1] 0 0 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1] 0.0 0.5 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   a_length_proportion(rep(\"CR\", 10), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop     10 (10.0%)          0                     Responders #> 2  prop_ci  (3.62, 16.38)          0 95% CI (Wald, with correction) a_length_proportion(factor(character(0)), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop       0 (0.0%)          0                     Responders #> 2  prop_ci   (0.00, 0.50)          0 95% CI (Wald, with correction)"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion estimation — estimate_proportion","title":"Proportion estimation — estimate_proportion","text":"analyze function estimate_proportion() creates layout element estimate proportion responders within studied population. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use constructing confidence interval proportion. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion estimation — estimate_proportion","text":"","code":"estimate_proportion(   lyt,   vars,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )  a_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion estimation — estimate_proportion","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights. variables (named list string) list additional analysis variables. long (flag) whether long description required. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"estimate_proportion\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (logical data.frame) logical vector used, indicates whether subject responder . TRUE represents successful outcome. data.frame provided, also strata variable names must provided variables list element strata strings. case data.frame, logical vector responses must indicated variable name .var. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion() table layout. s_proportion() returns statistics n_prop (n proportion) prop_ci (proportion CI) given variable. a_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion(): Statistics function estimating proportion along confidence interval. a_proportion(): Formatted analysis function used afun estimate_proportion().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/estimate_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion estimation — estimate_proportion","text":"","code":"dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = rep(LETTERS[1:3], each = 4),   AVAL    = rep(LETTERS[1:3], each = 4) )  basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_proportion(vars = \"AVAL\") %>%   build_table(df = dta_test) #>                                      A           B           C     #> —————————————————————————————————————————————————————————————————— #> Responders                       <Missing>   <Missing>   <Missing> #> 95% CI (Wald, with correction)   <Missing>   <Missing>   <Missing>  # Case with only logical vector. rsp_v <- c(1, 0, 1, 0, 1, 1, 0, 0) s_proportion(rsp_v) #> $n_prop #> [1] 4.0 0.5 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  9.102404 90.897596 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   # Example for Stratified Wilson CI nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  s_proportion(   df = dta,   .var = \"rsp\",   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"strat_wilson\" ) #> $n_prop #> [1] 49.00  0.49 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #>    lower    upper  #> 40.80675 56.65017  #> attr(,\"label\") #> [1] \"90% CI (Stratified Wilson, without correction)\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC data for examples — ex_data","title":"Simulated CDISC data for examples — ex_data","text":"Simulated CDISC data examples","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC data for examples — ex_data","text":"","code":"tern_ex_adsl  tern_ex_adae  tern_ex_adlb  tern_ex_adpp  tern_ex_adrs  tern_ex_adtte"},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC data for examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 21 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 42 columns. object class tbl_df (inherits tbl, data.frame) 4200 rows 50 columns. object class tbl_df (inherits tbl, data.frame) 522 rows 25 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 29 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 28 columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC data for examples — ex_data","text":"tern_ex_adsl: ADSL data tern_ex_adae: ADAE data tern_ex_adlb: ADLB data tern_ex_adpp: ADPP data tern_ex_adrs: ADRS data tern_ex_adtte: ADTTE data","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data — explicit_na","title":"Missing data — explicit_na","text":"Substitute missing data string factor level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data — explicit_na","text":"","code":"explicit_na(x, label = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data — explicit_na","text":"x (factor character) values missing values substituted. label (string) string missing data replaced .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data — explicit_na","text":"x NA values substituted label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Missing data — explicit_na","text":"","code":"explicit_na(c(NA, \"a\", \"b\")) #> [1] \"<Missing>\" \"a\"         \"b\"         is.na(explicit_na(c(NA, \"a\", \"b\"))) #> [1] FALSE FALSE FALSE  explicit_na(factor(c(NA, \"a\", \"b\"))) #> [1] <Missing> a         b         #> Levels: a b <Missing> is.na(explicit_na(factor(c(NA, \"a\", \"b\")))) #> [1] FALSE FALSE FALSE  explicit_na(sas_na(c(\"a\", \"\"))) #> [1] \"a\"         \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract elements by name — extract_by_name","title":"Extract elements by name — extract_by_name","text":"utility function extracts elements vector x names. Differences standard [ function :","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract elements by name — extract_by_name","text":"","code":"extract_by_name(x, names)"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract elements by name — extract_by_name","text":"x (named vector) extract named elements . names (character) vector names extract.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract elements by name — extract_by_name","text":"NULL x NULL, otherwise extracted elements x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_by_name.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract elements by name — extract_by_name","text":"x NULL, still always NULL returned (base function). x NULL, intersection names made names elements returned. , names appear x returned NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"Prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates, subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"extract_rsp_biomarkers(   variables,   data,   groups_lists = list(),   control = control_logistic(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (named list) controls response definition confidence level produced control_logistic(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_rsp, prop, , lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"can also specify continuous variable rsp use response_definition control convert internally logical variable reflecting binary response.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_biomarkers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\")  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in logistic regression models with one covariate `RACE`. The subgroups # are defined by the levels of `BMRKR2`. df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp      prop        or #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.8200000 0.9755036 #> 2       AGE                          Age   200   164 0.8200000 0.9952416 #> 3    BMRKR1 Continuous Level Biomarker 1    70    53 0.7571429 1.1524547 #> 4       AGE                          Age    70    53 0.7571429 0.9261012 #> 5    BMRKR1 Continuous Level Biomarker 1    68    58 0.8529412 0.8773122 #> 6       AGE                          Age    68    58 0.8529412 0.9867104 #> 7    BMRKR1 Continuous Level Biomarker 1    62    53 0.8548387 0.8792921 #> 8       AGE                          Age    62    53 0.8548387 1.0630262 #>         lcl      ucl conf_level      pval     pval_label     subgroup    var #> 1 0.8804862 1.080775       0.95 0.6352602 p-value (Wald) All Patients    ALL #> 2 0.9462617 1.046757       0.95 0.8530389 p-value (Wald) All Patients    ALL #> 3 0.9462127 1.403650       0.95 0.1584187 p-value (Wald)          LOW BMRKR2 #> 4 0.8487519 1.010500       0.95 0.0844837 p-value (Wald)          LOW BMRKR2 #> 5 0.7277189 1.057657       0.95 0.1699778 p-value (Wald)       MEDIUM BMRKR2 #> 6 0.8798911 1.106498       0.95 0.8189816 p-value (Wald)       MEDIUM BMRKR2 #> 7 0.7189748 1.075357       0.95 0.2103709 p-value (Wald)         HIGH BMRKR2 #> 8 0.9595973 1.177603       0.95 0.2418840 p-value (Wald)         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually, and we add a stratification # variable `STRATA1`. We also here use a continuous variable `EOSDY` # which is then binarized internally (response is defined as this variable # being larger than 750). df_grouped <- extract_rsp_biomarkers(   variables = list(     rsp = \"EOSDY\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\",     strata = \"STRATA1\"   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ),   control = control_logistic(     response_definition = \"I(response > 750)\"   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_rsp prop or lcl ucl conf_level #> 1    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 2       AGE                          Age   200     0    0 NA  NA  NA       0.95 #> 3    BMRKR1 Continuous Level Biomarker 1    70     0    0 NA  NA  NA       0.95 #> 4       AGE                          Age    70     0    0 NA  NA  NA       0.95 #> 5    BMRKR1 Continuous Level Biomarker 1   138     0    0 NA  NA  NA       0.95 #> 6       AGE                          Age   138     0    0 NA  NA  NA       0.95 #> 7    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 8       AGE                          Age   200     0    0 NA  NA  NA       0.95 #>   pval     pval_label        subgroup    var                    var_label #> 1   NA p-value (Wald)    All Patients    ALL                 All Patients #> 2   NA p-value (Wald)    All Patients    ALL                 All Patients #> 3   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 4   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 5   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 7   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #> 8   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2  content #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #> 7 analysis #> 8 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"Prepares response rates odds ratios population subgroups data frames. Simple wrapper h_odds_ratio_subgroups_df() h_proportion_subgroups_df(). Result list two data.frames: prop . variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"","code":"extract_rsp_subgroups(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_rsp_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"named list two elements: prop: data.frame containing columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. : data.frame containing columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables), optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"","code":"extract_survival_biomarkers(   variables,   data,   groups_lists = list(),   control = control_coxreg(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_tot_events, median, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"Prepares estimates median survival times treatment hazard ratios population subgroups data frames. Simple wrapper h_survtime_subgroups_df() h_coxph_subgroups_df(). Result list two data.frames: survtime hr. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"","code":"extract_survival_subgroups(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extract_survival_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"named list two elements: survtime: data.frame containing columns arm, n, n_events, median, subgroup, var, var_label, row_type. hr: data.frame containing columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values — extreme_format","title":"Format extreme values — extreme_format","text":"rtables formatting functions handle extreme values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(digits = 2L)  h_format_threshold(x, digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values — extreme_format","text":"digits (integer(1)) number decimal places display. x (numeric(1)) value format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values — extreme_format","text":"h_get_format_threshold() returns list 2 elements: threshold, low high thresholds, format_string, thresholds formatted strings. h_format_threshold() returns given value, value within digit threshold relation given value digit threshold, formatted string.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format extreme values — extreme_format","text":"input, apply format specified number digits. value threshold, returns \"<0.01\" e.g. number digits 2. value threshold, returns \">999.99\" e.g. number digits 2. zero, returns \"0.00\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Format extreme values — extreme_format","text":"h_get_format_threshold(): Internal helper function calculate threshold create formatted strings used Formatting Functions. Returns list elements threshold format_string. h_format_threshold(): Internal helper function apply threshold format value. Creates formatted string used Formatting Functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/extreme_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(2L) #> $threshold #>    low   high  #>   0.01 999.99  #>  #> $format_string #>       low      high  #>   \"<0.01\" \">999.99\"  #>   h_format_threshold(0.001) #> [1] \"<0.01\" h_format_threshold(1000) #> [1] \">999.99\""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for confidence interval — f_conf_level","text":"","code":"f_conf_level(conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for confidence interval — f_conf_level","text":"conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/f_conf_level.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for confidence interval — f_conf_level","text":"string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for p-value — f_pval","text":"","code":"f_pval(test_mean)"},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for p-value — f_pval","text":"test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/f_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for p-value — f_pval","text":"string.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse factor levels and keep only those new group levels — fct_collapse_only","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"collapses levels keeps new group levels, order provided. returned factor levels order given, possible missing level last (included missing values).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(.f, ..., .na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":".f (factor character) original vector. ... (named character) levels vector provided collapsed new level given respective name. .na_level (string) level use levels, missing new factor. Note level must contained new levels specified ....","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"modified factor collapsed levels. Values levels included given character vector input set missing level .na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"existing NAs input vector replaced missing level. needed, explicit_na() can called separately result.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_collapse_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(factor(c(\"a\", \"b\", \"c\", \"d\")), TRT = \"b\", CTRL = c(\"c\", \"d\")) #> [1] <Missing> TRT       CTRL      CTRL      #> Levels: TRT CTRL <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":null,"dir":"Reference","previous_headings":"","what":"Discard specified levels of a factor — fct_discard","title":"Discard specified levels of a factor — fct_discard","text":"discards observations well levels specified factor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(x, discard)"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Discard specified levels of a factor — fct_discard","text":"x (factor) original factor. discard (character) levels discard.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Discard specified levels of a factor — fct_discard","text":"modified factor observations well levels discard dropped.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_discard.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(factor(c(\"a\", \"b\", \"c\")), \"c\") #> [1] a b #> Levels: a b"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":null,"dir":"Reference","previous_headings":"","what":"Insertion of explicit missing values in a factor — fct_explicit_na_if","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"inserts explicit missing values factor based condition. Additionally, existing NA values explicitly converted given na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(x, condition, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"x (factor) original factor. condition (logical) positions insert missing values. na_level (string) level use missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"modified factor inserted existing NA converted na_level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fct_explicit_na_if.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(factor(c(\"a\", \"b\", NA)), c(TRUE, FALSE, FALSE)) #> [1] <Missing> b         <Missing> #> Levels: a b <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting functions for Cox proportional hazards regression — fit_coxreg","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"Fitting functions univariate multivariate Cox regression models.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"fit_coxreg_univar(variables, data, at = list(), control = control_coxreg())  fit_coxreg_multivar(variables, data, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"variables (named list) names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. data (data.frame) dataset containing variables fit models. (list numeric) candidate covariate numeric, use specify value covariate effect estimated. control (list) list parameters returned helper function control_coxreg().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar() returns coxreg.univar class object named list 5 elements: mod: Cox regression models fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model. : Value covariate effect estimated. fit_coxreg_multivar() returns coxreg.multivar class object named list 4 elements: mod: Cox regression model fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar(): Fit series univariate Cox regression models given inputs. fit_coxreg_multivar(): Fit multivariate Cox regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"using fit_coxreg_univar two study arms.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   # fit_coxreg_univar  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  ## Cox regression: arm + 1 covariate, stratified analysis. mod3 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", strata = \"covar2\",     covariates = c(\"covar1\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: no arm, only covariates. mod4 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # fit_coxreg_multivar  ## Cox regression: multivariate Cox regression. multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # Example without treatment arm. multivar_covs_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit for logistic regression — fit_logistic","title":"Fit for logistic regression — fit_logistic","text":"Fit (conditional) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit for logistic regression — fit_logistic","text":"","code":"fit_logistic(   data,   variables = list(response = \"Response\", arm = \"ARMCD\", covariates = NULL, interaction =     NULL, strata = NULL),   response_definition = \"response\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit for logistic regression — fit_logistic","text":"data (data.frame) data frame model fit. variables (named list string) list additional analysis variables. response_definition (string) definition event terms response. used fitting (conditional) logistic regression model left hand side formula.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit for logistic regression — fit_logistic","text":"fitted logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"model-specification","dir":"Reference","previous_headings":"","what":"Model Specification","title":"Fit for logistic regression — fit_logistic","text":"variables list needs include following elements: arm: Treatment arm variable name. response: response arm variable name. Usually 0/1 variable. covariates: either NULL (covariates) character vector covariate variable names. interaction: either NULL (interaction) string single covariate variable name already included covariates. interaction treatment arm included model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit for logistic regression — fit_logistic","text":"","code":"library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"fits Subgroup Treatment Effect Pattern logistic regression models binary (response) outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated odds ratios comparison second level vs. first one. (conditional) logistic regression model fit : response ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"fit_rsp_step(variables, data, control = c(control_step(), control_logistic()))"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"variables (named list character) list analysis variables: needs response, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_logistic().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_rsp_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"# Testing dataset with just two treatment arms. library(survival) library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(     PARAMCD == \"BESRSPI\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to have Placebo as reference arm for Odds Ratio calculations.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     RSP = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     SEX = factor(SEX)   )  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. # We use a large enough bandwidth to avoid too small subgroups and linear separation in those. step_matrix <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = 0.9)) ) dim(step_matrix) #> [1] 39 11 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.925        1.472755 #> [2,]             0.050                0            0.950        2.028546 #> [3,]             0.075                0            0.975        2.204086 #> [4,]             0.100                0            1.000        2.799776 #> [5,]             0.125                0            1.000        2.969998 #> [6,]             0.150                0            1.000        3.149068 #>      Interval Lower Interval Upper   n    logor       se   ci_lower ci_upper #> [1,]      0.4459546       11.74529 131 1.835008 1.134560 -0.3886885 4.058703 #> [2,]      0.4459546       12.73387 134 1.895158 1.136248 -0.3318481 4.122163 #> [3,]      0.4459546       14.75099 138 1.947699 1.136969 -0.2807193 4.176116 #> [4,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [5,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [6,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different logistic regression options, including confidence level. step_matrix2 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(conf_level = 0.9), control_step(bandwidth = NULL, degree = 1)) )  # Use a global constant model. This is helpful as a reference for the subgroup models. step_matrix3 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL, num_points = 2L)) )  # It is also possible to use strata, i.e. use conditional logistic regression models. variables2 <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\",   strata = c(\"STRATA1\", \"STRATA2\") )  step_matrix4 <- fit_rsp_step(   variables = variables2,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL)) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"fits subgroup treatment effect pattern (STEP) models survival outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated hazard ratios comparison second level vs. first one. model fit : Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"fit_survival_step(   variables,   data,   control = c(control_step(), control_coxph()) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"variables (named list character) list analysis variables: needs time, event, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_coxph().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/fit_survival_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"# Testing dataset with just two treatment arms. library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = \"Treatment Arm\", \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = c(\"AGE\", \"BMRKR2\"),   event = \"is_event\",   time = \"AVAL\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. step_matrix <- fit_survival_step(   variables = variables,   data = adtte_f ) dim(step_matrix) #> [1] 39 12 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.275        1.472755 #> [2,]             0.050                0            0.300        2.028546 #> [3,]             0.075                0            0.325        2.204086 #> [4,]             0.100                0            0.350        2.799776 #> [5,]             0.125                0            0.375        2.969998 #> [6,]             0.150                0            0.400        3.149068 #>      Interval Lower Interval Upper  n events      loghr        se   ci_lower #> [1,]      0.4459546       4.182444 39     29 0.03729601 0.4243013 -0.7943192 #> [2,]      0.4459546       4.349471 43     31 0.23246622 0.3881347 -0.5282639 #> [3,]      0.4459546       4.626913 46     32 0.07952492 0.3813113 -0.6678314 #> [4,]      0.4459546       4.805767 50     35 0.09020455 0.3638368 -0.6229026 #> [5,]      0.4459546       4.929816 53     37 0.15522702 0.3477999 -0.5264483 #> [6,]      0.4459546       5.020539 57     41 0.11135760 0.3332843 -0.5418676 #>       ci_upper #> [1,] 0.8689112 #> [2,] 0.9931963 #> [3,] 0.8268813 #> [4,] 0.8033117 #> [5,] 0.8369023 #> [6,] 0.7645828  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different Cox regression options. step_matrix2 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(conf_level = 0.9), control_step(degree = 2)) )  # Use a global model with cubic interaction and only 5 points. step_matrix3 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(), control_step(bandwidth = NULL, degree = 3, num_points = 5L)) )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"forest_viewport(   tbl,   width_row_names = NULL,   width_columns = NULL,   width_forest = grid::unit(1, \"null\"),   gap_column = grid::unit(1, \"lines\"),   gap_header = grid::unit(1, \"lines\"),   mat_form = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a viewport tree for the forest plot — forest_viewport","text":"tbl (VTableTree)rtables table object. width_row_names (grid::unit) width row names. width_columns (grid::unit) width column spans. width_forest (grid::unit) width forest plot. gap_column (grid::unit) gap width columns. gap_header (grid::unit) gap width header. mat_form (MatrixPrintForm) matrix print form table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a viewport tree for the forest plot — forest_viewport","text":"viewport tree.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/forest_viewport.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"library(grid)  tbl <- rtable(   header = rheader(     rrow(\"\", \"E\", rcell(\"CI\", colspan = 2)),     rrow(\"\", \"A\", \"B\", \"C\")   ),   rrow(\"row 1\", 1, 0.8, 1.1),   rrow(\"row 2\", 1.4, 0.8, 1.6),   rrow(\"row 3\", 1.2, 0.8, 1.2) )  # \\donttest{ v <- forest_viewport(tbl) #> Warning: `forest_viewport()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> Warning: `vp_forest_table_part()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>.  grid::grid.newpage() showViewport(v)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":null,"dir":"Reference","previous_headings":"","what":"Format automatically using data significant digits — format_auto","title":"Format automatically using data significant digits — format_auto","text":"Formatting function majority default methods used analyze_vars(). non-derived values, significant digits data used (e.g. range), derived values one digits (measure location dispersion like mean, standard deviation). function can called internally \"auto\" like, example, .formats = c(\"mean\" = \"auto\"). See details see works inner function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format automatically using data significant digits — format_auto","text":"","code":"format_auto(dt_var, x_stat)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format automatically using data significant digits — format_auto","text":"dt_var (numeric) variable data statistics calculated . Used find significant digits. analyze_vars comes .df_row (see rtables::additional_fun_params), row data row splits. column split considered. x_stat (string) string indicating current statistical method used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format automatically using data significant digits — format_auto","text":"string rtables prints table cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format automatically using data significant digits — format_auto","text":"internal function needed work rtables default structure format functions, .e. function(x, ...), x results statistical evaluation. can one element (e.g. .stats = \"mean_sd\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_auto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format automatically using data significant digits — format_auto","text":"","code":"x_todo <- c(0.001, 0.2, 0.0011000, 3, 4) res <- c(mean(x_todo[1:3]), sd(x_todo[1:3]))  # x is the result coming into the formatting function -> res!! format_auto(dt_var = x_todo, x_stat = \"mean_sd\")(x = res) #> [1] \"0.06737 (0.11486)\" format_auto(x_todo, \"range\")(x = range(x_todo)) #> [1] \"0.0010 - 4.0000\" no_sc_x <- c(0.0000001, 1) format_auto(no_sc_x, \"range\")(x = no_sc_x) #> [1] \"0.0000001 - 1.0000000\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction — format_count_fraction","title":"Format count and fraction — format_count_fraction","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction — format_count_fraction","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction — format_count_fraction","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.5)) #> [1] \"2 (50.0%)\" format_count_fraction_fixed_dp(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"Formats count together fraction special consideration count less 10.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"string format count (fraction %). count less 10, count printed.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_count_fraction_lt10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x = c(275, 0.9673)) #> [1] \"275 (96.7%)\" format_count_fraction_lt10(x = c(2, 0.6667)) #> [1] \"2\" format_count_fraction_lt10(x = c(9, 1)) #> [1] \"9\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a single extreme value — format_extreme_values","title":"Format a single extreme value — format_extreme_values","text":"Create formatting function single extreme value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_extreme_values(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a single extreme value — format_extreme_values","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a single extreme value — format_extreme_values","text":"rtables formatting function uses threshold digits return formatted extreme value.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_fun <- format_extreme_values(2L) format_fun(x = 0.127) #> [1] \"0.13\" format_fun(x = Inf) #> [1] \">999.99\" format_fun(x = 0) #> [1] \"0.00\" format_fun(x = 0.009) #> [1] \"<0.01\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values part of a confidence interval — format_extreme_values_ci","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"Formatting Function extreme values part confidence interval. Values formatted e.g. \"(xx.xx, xx.xx)\" number digits 2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_extreme_values_ci(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"rtables formatting function uses threshold digits return formatted extreme values confidence interval.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_extreme_values_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_fun <- format_extreme_values_ci(2L) format_fun(x = c(0.127, Inf)) #> [1] \"(0.13, >999.99)\" format_fun(x = c(0, 0.009)) #> [1] \"(0.00, <0.01)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage — format_fraction","title":"Format fraction and percentage — format_fraction","text":"Formats fraction together ratio percent.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage — format_fraction","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage — format_fraction","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x = c(num = 2L, denom = 3L)) #> [1] \"2/3 (66.7%)\" format_fraction(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"Formats fraction together ratio percent fixed single decimal place. Includes trailing zero case whole number percentages always keep one decimal place.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 4L)) #> [1] \"1/4 (25.0%)\" format_fraction_fixed_dp(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction with lower threshold — format_fraction_threshold","title":"Format fraction with lower threshold — format_fraction_threshold","text":"Formats fraction second element input x fraction. applies lower threshold, just stated fraction smaller .","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fraction_threshold(threshold)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction with lower threshold — format_fraction_threshold","text":"threshold (proportion) lower threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction with lower threshold — format_fraction_threshold","text":"rtables formatting function takes numeric input x second element fraction formatted. fraction equal threshold, displayed percentage. positive threshold, returns, e.g. \"<1\" threshold 0.01. zero, just \"0\" returned.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_fraction_threshold.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fun <- format_fraction_threshold(0.05) format_fun(x = c(20, 0.1)) #> [1] 10 format_fun(x = c(2, 0.01)) #> [1] \"<5\" format_fun(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":null,"dir":"Reference","previous_headings":"","what":"Format numeric values by significant figures — format_sigfig","title":"Format numeric values by significant figures — format_sigfig","text":"Format numeric values print specified number significant figures.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"format_sigfig(sigfig, format = \"xx\", num_fmt = \"fg\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format numeric values by significant figures — format_sigfig","text":"sigfig (integer(1)) number significant figures display. format (string) format label (string) apply printing value. Decimal places string ignored favor formatting significant figures. Formats options : \"xx\", \"xx / xx\", \"(xx, xx)\", \"xx - xx\", \"xx (xx)\". num_fmt (string) numeric format modifiers apply value. Defaults \"fg\" standard significant figures formatting - fixed (non-scientific notation) format (\"f\") sigfig equal number significant figures instead decimal places (\"g\"). See formatC() format argument options.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format numeric values by significant figures — format_sigfig","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_sigfig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"fmt_3sf <- format_sigfig(3) fmt_3sf(1.658) #> [1] \"1.66\" fmt_3sf(1e1) #> [1] \"10.0\"  fmt_5sf <- format_sigfig(5) fmt_5sf(0.57) #> [1] \"0.57000\" fmt_5sf(0.000025645) #> [1] \"0.000025645\""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":null,"dir":"Reference","previous_headings":"","what":"Format XX as a formatting function — format_xx","title":"Format XX as a formatting function — format_xx","text":"Translate string x dots interpreted number place holders, others formatting elements.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format XX as a formatting function — format_xx","text":"","code":"format_xx(str)"},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format XX as a formatting function — format_xx","text":"str (string) template.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format XX as a formatting function — format_xx","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/format_xx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format XX as a formatting function — format_xx","text":"","code":"test <- list(c(1.658, 0.5761), c(1e1, 785.6))  z <- format_xx(\"xx (xx.x)\") sapply(test, z) #> [1] \"2 (0.6)\"    \"10 (785.6)\"  z <- format_xx(\"xx.x - xx.x\") sapply(test, z) #> [1] \"1.7 - 0.6\"  \"10 - 785.6\"  z <- format_xx(\"xx.x, incl. xx.x% NE\") sapply(test, z) #> [1] \"1.7, incl. 0.6% NE\"  \"10, incl. 785.6% NE\""},{"path":"https://insightsengineering.github.io/tern/main/reference/formatting_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Formatting functions — formatting_functions","title":"Formatting functions — formatting_functions","text":"See list formatting functions created tern work rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/formatting_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Formatting functions — formatting_functions","text":"available formats can listed via formatters::list_valid_format_labels(). Additional custom formats can created via formatters::sprintf_format() function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman plot — g_bland_altman","title":"Bland-Altman plot — g_bland_altman","text":"Graphing function produces Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman plot — g_bland_altman","text":"","code":"g_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman plot — g_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman plot — g_bland_altman","text":"ggplot Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman plot — g_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  g_bland_altman(x = x, y = y, conf_level = 0.9)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a forest plot from an rtable — g_forest","text":"","code":"g_forest(   tbl,   col_x = attr(tbl, \"col_x\"),   col_ci = attr(tbl, \"col_ci\"),   vline = 1,   forest_header = attr(tbl, \"forest_header\"),   xlim = c(0.1, 10),   logx = TRUE,   x_at = c(0.1, 1, 10),   width_row_names = lifecycle::deprecated(),   width_columns = NULL,   width_forest = lifecycle::deprecated(),   lbl_col_padding = 0,   rel_width_forest = 0.25,   font_size = 12,   col_symbol_size = attr(tbl, \"col_symbol_size\"),   col = getOption(\"ggplot2.discrete.colour\")[1],   ggtheme = NULL,   as_list = FALSE,   gp = lifecycle::deprecated(),   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a forest plot from an rtable — g_forest","text":"tbl (VTableTree)rtables table least one column single value one column 2 values. col_x (integer(1) NULL) column index estimator. default tries get tbl attribute col_x, otherwise needs manually specified. NULL, points excluded forest plot. col_ci (integer(1) NULL) column index confidence intervals. default tries get tbl attribute col_ci, otherwise needs manually specified. NULL, lines excluded forest plot. vline (numeric(1) NULL) x coordinate vertical line, NULL line omitted. forest_header (character(2)) text displayed left right vline, respectively. vline = NULL forest_header printed. default tries get tbl attribute forest_header. NULL, defaults extracted table possible, set \"Comparison\\nBetter\" \"Treatment\\nBetter\" . xlim (numeric(2)) limits x axis. logx (flag) show x-values logarithm scale. x_at (numeric) x-tick locations, NULL, x_at set vline xlim values. width_row_names Please use lbl_col_padding argument instead. width_columns (numeric) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. width_forest Please use rel_width_forest argument instead. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. col_symbol_size (numeric NULL) column index tbl containing data used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. default tries get tbl attribute col_symbol_size, otherwise needs manually specified. col (character) color(s). ggtheme (theme) graphical theme provided ggplot2 control styling plot. as_list (flag) whether two ggplot objects returned list. TRUE, named list two elements, table plot, returned. FALSE (default) table forest plot printed side--side via cowplot::plot_grid(). gp g_forest now generated ggplot object. argument longer used. draw g_forest now generated ggplot object. argument longer used. newpage g_forest now generated ggplot object. argument longer used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a forest plot from an rtable — g_forest","text":"ggplot forest plot table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a forest plot from an rtable — g_forest","text":"Given rtables::rtable() object least one column single value one column 2 values, converts table ggplot2::ggplot() object generates accompanying forest plot. table forest plot printed side--side.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_forest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a forest plot from an rtable — g_forest","text":"","code":"library(dplyr) library(forcats) library(nestcolor)  adrs <- tern_ex_adrs n_records <- 20 adrs_labels <- formatters::var_labels(adrs, fill = TRUE) adrs <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   slice(seq_len(n_records)) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs) <- c(adrs_labels, \"Response\") df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"STRATA2\")),   data = adrs ) # Full commonly used response table.  tbl <- basic_table() %>%   tabulate_rsp_subgroups(df) g_forest(tbl)   # Odds ratio only table.  tbl_or <- basic_table() %>%   tabulate_rsp_subgroups(df, vars = c(\"n_tot\", \"or\", \"ci\")) g_forest(   tbl_or,   forest_header = c(\"Comparison\\nBetter\", \"Treatment\\nBetter\") )   # Survival forest plot example. adtte <- tern_ex_adtte # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = TRUE) adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- list(   \"ARM\" = adtte_labels[\"ARM\"],   \"SEX\" = adtte_labels[\"SEX\"],   \"AVALU\" = adtte_labels[\"AVALU\"],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- as.character(labels) df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) table_hr <- basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) g_forest(table_hr)   # Works with any `rtable`. tbl <- rtable(   header = c(\"E\", \"CI\", \"N\"),   rrow(\"\", 1, c(.8, 1.2), 200),   rrow(\"\", 1.2, c(1.1, 1.4), 50) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   col_symbol_size = 3 )   tbl <- rtable(   header = rheader(     rrow(\"\", rcell(\"A\", colspan = 2)),     rrow(\"\", \"c1\", \"c2\")   ),   rrow(\"row 1\", 1, c(.8, 1.2)),   rrow(\"row 2\", 1.2, c(1.1, 1.4)) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   vline = 1,   forest_header = c(\"Hello\", \"World\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual patient plots — g_ipp","title":"Individual patient plots — g_ipp","text":"Line plot(s) displaying trend patients' parameter values time rendered. Patients' individual baseline values can added plot(s) reference.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual patient plots — g_ipp","text":"","code":"g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var = \"USUBJID\",   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   plotting_choices = c(\"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\"),   max_obs_per_plot = 4,   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Individual patient plots — g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. plotting_choices (string) specifies options displaying plots. Must one \"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\". max_obs_per_plot (integer(1)) number observations plotted one plot. Ignored plotting_choices \"separate_by_obs\". col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Individual patient plots — g_ipp","text":"ggplot object list ggplot objects.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Individual patient plots — g_ipp","text":"g_ipp(): Plotting function individual patient plots , depending user preference, renders single graphic compiles list graphics show trends individual's parameter values time.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Individual patient plots — g_ipp","text":"","code":"library(dplyr) library(nestcolor)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  plot_list <- g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   ylab = \"SGOT/ALT (U/L)\",   title = \"Individual Patient Plots\",   add_baseline_hline = TRUE,   plotting_choices = \"split_by_max_obs\",   max_obs_per_plot = 5 ) plot_list #> [[1]]  #>  #> [[2]]  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Kaplan-Meier plot — g_km","title":"Kaplan-Meier plot — g_km","text":"survival model, graphic rendered along tabulated annotation including number patient risk given time median survival per group.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kaplan-Meier plot — g_km","text":"","code":"g_km(   df,   variables,   control_surv = control_surv_timepoint(),   col = NULL,   lty = NULL,   lwd = 0.5,   censor_show = TRUE,   pch = 3,   size = 2,   max_time = NULL,   xticks = NULL,   xlab = \"Days\",   yval = c(\"Survival\", \"Failure\"),   ylab = paste(yval, \"Probability\"),   ylim = NULL,   title = NULL,   footnotes = NULL,   font_size = 10,   ci_ribbon = FALSE,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE,   annot_surv_med = TRUE,   annot_coxph = FALSE,   annot_stats = NULL,   annot_stats_vlines = FALSE,   control_coxph_pw = control_coxph(),   ref_group_coxph = NULL,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(),   legend_pos = NULL,   rel_height_plot = 0.75,   ggtheme = NULL,   as_list = FALSE,   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated(),   gp = lifecycle::deprecated(),   vp = lifecycle::deprecated(),   name = lifecycle::deprecated(),   annot_coxph_ref_lbls = lifecycle::deprecated(),   position_coxph = lifecycle::deprecated(),   position_surv_med = lifecycle::deprecated(),   width_annots = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kaplan-Meier plot — g_km","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. control_surv (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string)\"plain\" (default), \"log\", \"log-log\" confidence interval type, see survival::survfit(). Note option \"none\" longer supported. col (character) lines colors. Length vector equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). censor_show (flag) whether show censored observations. pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. xlab (string) x-axis label. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. font_size (numeric(1)) font size use text. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. annot_stats (string NULL) statistics annotations add plot. Options median (median survival follow-time) min (minimum survival follow-time). annot_stats_vlines (flag) add vertical lines corresponding statistics specified annot_stats. annot_stats NULL lines added. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot. as_list (flag) whether two ggplot objects returned list annot_at_risk = TRUE. TRUE, named list two elements, plot table, returned. FALSE (default) patients risk table printed plot via cowplot::plot_grid(). draw function longer generates grob objects. newpage function longer generates grob objects. gp function longer generates grob objects. vp function longer generates grob objects. name function longer generates grob objects. annot_coxph_ref_lbls Please use ref_lbls element control_annot_coxph instead. position_coxph Please use x y elements control_annot_coxph instead. position_surv_med Please use x y elements control_annot_surv_med instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\"","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Kaplan-Meier plot — g_km","text":"ggplot Kaplan-Meier plot (optionally) summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kaplan-Meier plot — g_km","text":"","code":"library(dplyr) library(nestcolor)  df <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) variables <- list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\")  # Basic examples g_km(df = df, variables = variables)  g_km(df = df, variables = variables, yval = \"Failure\")   # Examples with customization parameters applied g_km(   df = df,   variables = variables,   control_surv = control_surv_timepoint(conf_level = 0.9),   col = c(\"grey25\", \"grey50\", \"grey75\"),   annot_at_risk_title = FALSE,   lty = 1:3,   font_size = 8 )  g_km(   df = df,   variables = variables,   annot_stats = c(\"min\", \"median\"),   annot_stats_vlines = TRUE,   max_time = 3000,   ggtheme = ggplot2::theme_minimal() )   # Example with pairwise Cox-PH analysis annotation table, adjusted annotation tables g_km(   df = df, variables = variables,   annot_coxph = TRUE,   control_coxph = control_coxph(pval_method = \"wald\", ties = \"exact\", conf_level = 0.99),   control_annot_coxph = control_coxph_annot(x = 0.26, w = 0.35),   control_annot_surv_med = control_surv_med_annot(x = 0.8, y = 0.9, w = 0.35) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot with optional table — g_lineplot","title":"Line plot with optional table — g_lineplot","text":"Line plot optional table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot with optional table — g_lineplot","text":"","code":"g_lineplot(   df,   alt_counts_df = NULL,   variables = control_lineplot_vars(),   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = NULL,   sfun = s_summary,   ...,   mid_type = \"pl\",   mid_point_size = 2,   position = ggplot2::position_dodge(width = 0.4),   legend_title = NULL,   legend_position = \"bottom\",   ggtheme = nestcolor::theme_nest(),   xticks = NULL,   xlim = NULL,   ylim = NULL,   x_lab = obj_label(df[[variables[[\"x\"]]]]),   y_lab = NULL,   y_lab_add_paramcd = TRUE,   y_lab_add_unit = TRUE,   title = \"Plot of Mean and 95% Confidence Limits by Visit\",   subtitle = \"\",   subtitle_add_paramcd = TRUE,   subtitle_add_unit = TRUE,   caption = NULL,   table_format = NULL,   table_labels = NULL,   table_font_size = 3,   errorbar_width = 0.45,   newpage = lifecycle::deprecated(),   col = NULL,   linetype = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot with optional table — g_lineplot","text":"df (data.frame) data set containing analysis variables. alt_counts_df (data.frame NULL) data set used () counts objects groups stratification. variables (named character) vector variable names df include: x (string) name x-axis variable. y (string) name y-axis variable. group_var (string NULL) name grouping variable (strata), .e. treatment arm. Can NA indicate lack groups. subject_var (string NULL) name subject variable. applies group_var NULL. paramcd (string NA) name variable parameter's code. Used y-axis label plot's subtitle. Can NA paramcd added y-axis label subtitle. y_unit (string NA) name variable units y. Used y-axis label plot's subtitle. Can NA y unit added y-axis label subtitle. facet_var (string NA) name secondary grouping variable used plot faceting, .e. treatment arm. Can NA indicate lack groups. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. sfun (function) function compute values required statistics. must return named list atomic vectors. names list elements refer names statistics used mid, interval, table. must able accept input vector data statistics computed. ... optional arguments sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. position (character call) geom element position adjustment, either string, result call position adjustment function. legend_title (string) legend title. legend_position (string) position plot legend (\"none\", \"left\", \"right\", \"bottom\", \"top\", two-element numeric vector). ggtheme (theme) graphical theme provided ggplot2 control styling plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis, use variables$x numeric. NULL (default), labeling::extended() used determine optimal tick positions x-axis. variables$x numeric, argument ignored. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. x_lab (string NULL) x-axis label. NULL label added. y_lab (string NULL) y-axis label. NULL label added. y_lab_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added y-axis label (y_lab). y_lab_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added y-axis label (y_lab). title (string) plot title. subtitle (string) plot subtitle. subtitle_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added plot's subtitle (subtitle). subtitle_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added plot's subtitle (subtitle). caption (string) optional caption plot. table_format (named character NULL) format patterns descriptive statistics used (optional) table appended plot. passed directly h_format_row function format parameter. Names table_format must match names statistics returned sfun function. table_labels (named character NULL) labels descriptive statistics used (optional) table appended plot. Names table_labels must match names statistics returned sfun function. table_font_size (numeric(1)) font size text table. errorbar_width (numeric(1)) width error bars. newpage used. col (character) color(s). See ?ggplot2::aes_colour_fill_alpha example values. linetype (character) line type(s). See ?ggplot2::aes_linetype_size_shape example values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot with optional table — g_lineplot","text":"ggplot line plot (statistics table applicable).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot with optional table — g_lineplot","text":"","code":"library(nestcolor)  adsl <- tern_ex_adsl adlb <- tern_ex_adlb %>% dplyr::filter(ANL01FL == \"Y\", PARAMCD == \"ALT\", AVISIT != \"SCREENING\") adlb$AVISIT <- droplevels(adlb$AVISIT) adlb <- dplyr::mutate(adlb, AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min))  # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\")   # Mean with CI, no stratification with group_var g_lineplot(adlb, variables = control_lineplot_vars(group_var = NA))   # Mean, upper whisker of CI, no group_var(strata) counts N g_lineplot(   adlb,   whiskers = \"mean_ci_upr\",   title = \"Plot of Mean and Upper 95% Confidence Limit by Visit\" )   # Median with CI g_lineplot(   adlb,   adsl,   mid = \"median\",   interval = \"median_ci\",   whiskers = c(\"median_ci_lwr\", \"median_ci_upr\"),   title = \"Plot of Median and 95% Confidence Limits by Visit\" )   # Mean, +/- SD g_lineplot(adlb, adsl,   interval = \"mean_sdi\",   whiskers = c(\"mean_sdi_lwr\", \"mean_sdi_upr\"),   title = \"Plot of Median +/- SD by Visit\" )   # Mean with CI plot with stats table g_lineplot(adlb, adsl, table = c(\"n\", \"mean\", \"mean_ci\"))   # Mean with CI, table and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   control = control_analyze_vars(conf_level = 0.80),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )   # Mean with CI, table, filtered data adlb_f <- dplyr::filter(adlb, ARMCD != \"ARM A\" | AVISIT == \"BASELINE\") g_lineplot(adlb_f, table = c(\"n\", \"mean\"))"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a STEP graph — g_step","title":"Create a STEP graph — g_step","text":"Based STEP results, creates ggplot graph showing estimated HR along continuous biomarker value subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a STEP graph — g_step","text":"","code":"g_step(   df,   use_percentile = \"Percentile Center\" %in% names(df),   est = list(col = \"blue\", lty = 1),   ci_ribbon = list(fill = getOption(\"ggplot2.discrete.colour\")[1], alpha = 0.5),   col = getOption(\"ggplot2.discrete.colour\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a STEP graph — g_step","text":"df (tibble) result tidy.step(). use_percentile (flag) whether use percentiles x axis actual biomarker values. est (named list)col lty settings estimate line. ci_ribbon (named list NULL)fill alpha settings confidence interval ribbon area, NULL plot CI ribbon. col (character) color(s).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a STEP graph — g_step","text":"ggplot STEP graph.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/g_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a STEP graph — g_step","text":"","code":"library(nestcolor) library(survival) lung$sex <- factor(lung$sex)  # Survival example. vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) step_data <- broom::tidy(step_matrix)  # Default plot. g_step(step_data)   # Add the reference 1 horizontal line. library(ggplot2) g_step(step_data) +   ggplot2::geom_hline(ggplot2::aes(yintercept = 1), linetype = 2)   # Use actual values instead of percentiles, different color for estimate and no CI, # use log scale for y axis. g_step(   step_data,   use_percentile = FALSE,   est = list(col = \"blue\", lty = 1),   ci_ribbon = NULL ) + scale_y_log10()   # Adding another curve based on additional column. step_data$extra <- exp(step_data$`Percentile Center`) g_step(step_data) +   ggplot2::geom_line(ggplot2::aes(y = extra), linetype = 2, color = \"green\")   # Response example. vars <- list(   response = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_rsp_step(   variables = vars,   data = lung,   control = c(     control_logistic(response_definition = \"I(response == 2)\"),     control_step()   ) ) step_data <- broom::tidy(step_matrix) g_step(step_data)"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Horizontal waterfall plot — g_waterfall","title":"Horizontal waterfall plot — g_waterfall","text":"basic waterfall plot visualizes quantity height ordered value markup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"g_waterfall(   height,   id,   col_var = NULL,   col = getOption(\"ggplot2.discrete.colour\"),   xlab = NULL,   ylab = NULL,   col_legend_title = NULL,   title = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Horizontal waterfall plot — g_waterfall","text":"height (numeric) vector containing values plotted waterfall bars. id (character) vector containing identifiers use x-axis label waterfall bars. col_var (factor, character, NULL) categorical variable bar coloring. NULL default. col (character) color(s). xlab (string) x label. Default \"ID\". ylab (string) y label. Default \"Value\". col_legend_title (string) text displayed legend title. title (string) text displayed plot title.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Horizontal waterfall plot — g_waterfall","text":"ggplot waterfall plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"library(dplyr) library(nestcolor)  g_waterfall(height = c(3, 5, -1), id = letters[1:3])   g_waterfall(   height = c(3, 5, -1),   id = letters[1:3],   col_var = letters[1:3] )   adsl_f <- tern_ex_adsl %>%   select(USUBJID, STUDYID, ARM, ARMCD, SEX)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"OVRINV\") %>%   mutate(pchg = rnorm(n(), 10, 50))  adrs_f <- head(adrs_f, 30) adrs_f <- adrs_f[!duplicated(adrs_f$USUBJID), ] head(adrs_f) #> # A tibble: 5 × 30 #>   STUDYID COUNTRY SITEID SUBJID   AGE SEX   ARMCD ARM      ACTARMCD ACTARM RACE  #>   <chr>   <fct>   <chr>  <chr>  <dbl> <fct> <fct> <fct>    <fct>    <fct>  <fct> #> 1 AB12345 BRA     BRA-1  id-105  37.8 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> 2 AB12345 BRA     BRA-1  id-171  29.8 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 3 AB12345 BRA     BRA-1  id-177  38.9 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 4 AB12345 BRA     BRA-1  id-23   41.3 F     ARM A A: Drug… ARM A    A: Dr… AMER… #> 5 AB12345 BRA     BRA-1  id-59   26.7 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> # ℹ 19 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>, EOSDY <dbl>, #> #   STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, REGION1 <fct>, #> #   SAFFL <fct>, USUBJID <chr>, AVISIT <fct>, PARAMCD <fct>, PARAM <fct>, #> #   AVALC <fct>, AVAL <int>, ADTM <date>, AVISITN <dbl>, DTHFL <fct>, #> #   pchg <dbl>  g_waterfall(   height = adrs_f$pchg,   id = adrs_f$USUBJID,   col_var = adrs_f$AVALC )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   col_var = adrs_f$SEX )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   xlab = \"ID\",   ylab = \"Percentage Change\",   title = \"Waterfall plot\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to return a named list of covariate names — get_covariates","title":"Utility function to return a named list of covariate names — get_covariates","text":"Utility function return named list covariate names","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to return a named list of covariate names — get_covariates","text":"","code":"get_covariates(covariates)"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to return a named list of covariate names — get_covariates","text":"covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_covariates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to return a named list of covariate names — get_covariates","text":"named list character vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":null,"dir":"Reference","previous_headings":"","what":"Smooth function with optional grouping — get_smooths","title":"Smooth function with optional grouping — get_smooths","text":"produces loess smoothed estimates y Student confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Smooth function with optional grouping — get_smooths","text":"","code":"get_smooths(df, x, y, groups = NULL, level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Smooth function with optional grouping — get_smooths","text":"df (data.frame) data set containing analysis variables. x (string) x column name. y (string) y column name. groups (character NULL) vector optional grouping variables names. level (proportion) level confidence interval use (0.95 default).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/get_smooths.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Smooth function with optional grouping — get_smooths","text":"data.frame original x, smoothed y, ylow, yhigh, optional groups variables formatted factor type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert list of groups to a data frame — groups_list_to_df","title":"Convert list of groups to a data frame — groups_list_to_df","text":"converts list group levels data frame format expected rtables::add_combo_levels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"groups_list_to_df(groups_list)"},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert list of groups to a data frame — groups_list_to_df","text":"groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert list of groups to a data frame — groups_list_to_df","text":"tibble required format.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/groups_list_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"grade_groups <- list(   \"Any Grade (%)\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 3-4 (%)\" = c(\"3\", \"4\"),   \"Grade 5 (%)\" = \"5\" ) groups_list_to_df(grade_groups) #> # A tibble: 3 × 4 #>   valname  label         levelcombo exargs     #>   <chr>    <chr>         <list>     <list>     #> 1 AnyGrade Any Grade (%) <chr [5]>  <list [0]> #> 2 Grade34  Grade 3-4 (%) <chr [2]>  <list [0]> #> 3 Grade5   Grade 5 (%)   <chr [1]>  <list [0]>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"Helper function prepare ADLB data frame used input count_abnormal_by_worst_grade(). following pre-processing steps applied: adlb filtered variable avisit include post-baseline visits. adlb filtered variables worst_flag_low worst_flag_high worst grades (either direction) included. standard lab grade variable atoxgr, following two variables derived added adlb: grade direction variable (e.g. GRADE_DIR). variable takes value \"HIGH\" atoxgr > 0, \"LOW\" atoxgr < 0, \"ZERO\" otherwise. toxicity grade variable (e.g. GRADE_ANL) negative values atoxgr replaced absolute values. Unused factor levels dropped adlb via droplevels().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(   adlb,   atoxgr = \"ATOXGR\",   avisit = \"AVISIT\",   worst_flag_low = \"WGRLOFL\",   worst_flag_high = \"WGRHIFL\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"adlb (data.frame) ADLB data frame. atoxgr (string) name analysis toxicity grade variable. must factor variable. avisit (string) name analysis visit variable. worst_flag_low (string) name worst low lab grade flag variable. variable set \"Y\" indicating records worst low lab grades. worst_flag_high (string) name worst high lab grade flag variable. variable set \"Y\" indicating records worst high lab grades.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"h_adlb_abnormal_by_worst_grade() returns adlb data frame two new variables: GRADE_DIR GRADE_ANL.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(tern_ex_adlb) %>%   dplyr::select(ATOXGR, GRADE_DIR, GRADE_ANL) %>%   head(10) #> # A tibble: 10 × 3 #>    ATOXGR GRADE_DIR GRADE_ANL #>    <fct>  <fct>     <fct>     #>  1 -3     LOW       3         #>  2 0      ZERO      0         #>  3 0      ZERO      0         #>  4 2      HIGH      2         #>  5 0      ZERO      0         #>  6 0      ZERO      0         #>  7 -4     LOW       4         #>  8 1      HIGH      1         #>  9 -1     LOW       1         #> 10 0      ZERO      0"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"Helper function prepare df generate patient count shift table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"h_adlb_worsen(   adlb,   worst_flag_low = NULL,   worst_flag_high = NULL,   direction_var )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"adlb (data.frame) ADLB data frame. worst_flag_low (named vector) worst low post-baseline lab grade flag variable. See implemented following examples. worst_flag_high (named vector) worst high post-baseline lab grade flag variable. See implemented following examples. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"h_adlb_worsen() returns adlb data.frame containing worst labs specified according worst_flag_low worst_flag_high direction specified according direction_var. instance, lab needed low direction , records flagged worst_flag_low selected. lab needed low high directions, worst low records selected low direction, worst high record selected high direction.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adlb_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"Helper function merges ADSL ADLB datasets missing lab test records inserted output dataset. Remember na_level must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"h_adsl_adlb_merge_using_worst_flag(   adsl,   adlb,   worst_flag = c(WGRHIFL = \"Y\"),   by_visit = FALSE,   no_fillin_visits = c(\"SCREENING\", \"BASELINE\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"adsl (data.frame) ADSL data frame. adlb (data.frame) ADLB data frame. worst_flag (named character) worst post-baseline lab flag variable. See implemented following examples. by_visit (flag) defaults FALSE generate worst grade per patient. worst grade per patient per visit specified worst_flag, by_visit TRUE generate worst grade patient per visit. no_fillin_visits (named character) visits considered post-baseline worst toxicity grade. Defaults c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"df containing variables shared adlb adsl along variables PARAM, PARAMCD, ATOXGR, BTOXGR relevant analysis. Optionally, AVISIT AVISITN included by_visit = TRUE no_fillin_visits = c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"result data missing records created following situations: Patients present adsl lab data adlb (baseline post-baseline). Patients post-baseline lab values. Patients without post-baseline values flagged worst.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"# `h_adsl_adlb_merge_using_worst_flag` adlb_out <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRHIFL\" = \"Y\") )  # `h_adsl_adlb_merge_using_worst_flag` by visit example adlb_out_by_visit <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRLOVFL\" = \"Y\"),   by_visit = TRUE )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(.var, .df_row, variables, interaction_item = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to return results of a linear model — h_ancova","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to return results of a linear model — h_ancova","text":"summary linear model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(   .var = \"Sepal.Length\",   .df_row = iris,   variables = list(arm = \"Species\", covariates = c(\"Petal.Length * Petal.Width\", \"Sepal.Width\")) ) #>  Species    emmean     SE  df lower.CL upper.CL #>  setosa       6.15 0.3370 143     5.49     6.82 #>  versicolor   5.72 0.0668 143     5.59     5.85 #>  virginica    5.41 0.1490 143     5.11     5.70 #>  #> Confidence level used: 0.95"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Helper function s_count_occurrences_by_grade() insert grade groupings list individual grade frequencies. order final result follows order grade_groups. elements -grade group (), .e. grade group equal refs moved end. Grade groups names must unique.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   grade_groups,   refs,   remove_single = TRUE,   only_grade_groups = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"grade_groups (named list character) list containing groupings grades. refs (named list numeric) named list name corresponds reference grade level entry represents count. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Formatted list grade groupings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_append_grade_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade 1-2` #> [1] 30 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 20 #>  #> $`Grade 3-4` #> [1] 70 #>  #> $`3` #> [1] 30 #>  #> $`4` #> [1] 40 #>  #> $`5` #> [1] 50 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(5:1),     \"Grade A\" = \"5\",     \"Grade B\" = c(\"4\", \"3\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade A` #> [1] 50 #>  #> $`Grade B` #> [1] 70 #>  #> $`4` #> [1] 40 #>  #> $`3` #> [1] 30 #>  #> $`2` #> [1] 20 #>  #> $`1` #> [1] 10 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 5, \"3\" = 0) ) #> $`Any Grade` #> [1] 15 #>  #> $`Grade 1-2` #> [1] 15 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 5 #>  #> $`Grade 3-4` #> [1] 0 #>  #> $`3` #> [1] 0 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain column indices — h_col_indices","title":"Obtain column indices — h_col_indices","text":"Helper function extract column indices VTableTree given vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain column indices — h_col_indices","text":"","code":"h_col_indices(table_tree, col_names)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain column indices — h_col_indices","text":"table_tree (VTableTree)rtables table object extract indices . col_names (character) vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_col_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain column indices — h_col_indices","text":"vector column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_cumulative() — h_count_cumulative","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"Helper function calculate count fraction x values lower upper tail given threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"h_count_cumulative(   x,   threshold,   lower_tail = TRUE,   include_eq = TRUE,   na.rm = TRUE,   .N_col )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"x (numeric) vector numbers want analyze. threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"named vector items: count: count values less , less equal , greater , greater equal threshold user specification. fraction: fraction count.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"set.seed(1, kind = \"Mersenne-Twister\") x <- c(sample(1:10, 10), NA) .N_col <- length(x)  h_count_cumulative(x, 5, .N_col = .N_col) #>     count  fraction  #> 5.0000000 0.4545455  h_count_cumulative(x, 5, lower_tail = FALSE, include_eq = FALSE, na.rm = FALSE, .N_col = .N_col) #>     count  fraction  #> 6.0000000 0.5454545  h_count_cumulative(x, 0, lower_tail = FALSE, .N_col = .N_col) #>      count   fraction  #> 10.0000000  0.9090909  h_count_cumulative(x, 100, lower_tail = FALSE, .N_col = .N_col) #>    count fraction  #>        0        0"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Cox proportional hazards regression — h_cox_regression","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"Helper functions used fit_coxreg_univar() fit_coxreg_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"h_coxreg_univar_formulas(variables, interaction = FALSE)  h_coxreg_multivar_formula(variables)  h_coxreg_univar_extract(effect, covar, data, mod, control = control_coxreg())  h_coxreg_multivar_extract(var, data, mod, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"variables (named list string) list additional analysis variables. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE. effect (string) treatment variable. covar (string) name covariate model. data (data.frame) dataset containing variables summarize. mod (coxph) Cox regression model fitted survival::coxph(). control (list) list controls returned control_coxreg(). var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas() returns character vector coercible formulas (e.g stats::.formula()). h_coxreg_multivar_formula() returns string coercible formula (e.g stats::.formula()). h_coxreg_univar_extract() returns data.frame variables effect, term, term_label, level, n, hr, lcl, ucl, pval. h_coxreg_multivar_extract() returns data.frame variables pval, hr, lcl, ucl, level, n, term, term_label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas(): Helper Cox regression formula. Creates list formulas. used internally fit_coxreg_univar() comparison univariate Cox regression models. h_coxreg_multivar_formula(): Helper multivariate Cox regression formula. Creates formulas string. used internally fit_coxreg_multivar() comparison multivariate Cox regression models. Interactions included multivariate Cox regression model. h_coxreg_univar_extract(): Utility function help tabulate result univariate Cox regression model. h_coxreg_multivar_extract(): Tabulation multivariate Cox regressions. Utility function help tabulate result multivariate Cox regression model treatment/covariate variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"# `h_coxreg_univar_formulas`  ## Simple formulas. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\")   ) ) #>                                        ref  #>     \"survival::Surv(time, status) ~ armcd\"  #>                                          X  #> \"survival::Surv(time, status) ~ armcd + X\"  #>                                          y  #> \"survival::Surv(time, status) ~ armcd + y\"   ## Addition of an optional strata. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ) ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd + X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd + y + strata(SITE)\"   ## Inclusion of the interaction term. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ),   interaction = TRUE ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd * X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd * y + strata(SITE)\"   ## Only covariates fitted in separate models. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", covariates = c(\"X\", \"y\")   ) ) #>                                      X                                      y  #> \"survival::Surv(time, status) ~ 1 + X\" \"survival::Surv(time, status) ~ 1 + y\"   # `h_coxreg_multivar_formula`  h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\")   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE\"  # Addition of an optional strata. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE + strata(SITE)\"  # Example without treatment arm. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ 1 + RACE + AGE + strata(SITE)\"  library(survival)  dta_simple <- data.frame(   time = c(5, 5, 10, 10, 5, 5, 10, 10),   status = c(0, 0, 1, 0, 0, 1, 1, 1),   armcd = factor(LETTERS[c(1, 1, 1, 1, 2, 2, 2, 2)], levels = c(\"A\", \"B\")),   var1 = c(45, 55, 65, 75, 55, 65, 85, 75),   var2 = c(\"F\", \"M\", \"F\", \"M\", \"F\", \"M\", \"F\", \"U\") ) mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_univar_extract(   effect = \"armcd\", covar = \"armcd\", mod = mod, data = dta_simple ) result #>       effect  term       term_label level n       hr       lcl      ucl #> 1 Treatment: armcd B vs control (A)     B 8 6.551448 0.4606904 93.16769 #>       pval #> 1 0.165209  mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_multivar_extract(   var = \"var1\", mod = mod, data = dta_simple ) result #>        pval        hr      lcl      ucl level n term term_label #> 2 0.4456195 0.9423284 0.808931 1.097724  var1 8 var1       var1"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to tidy survival fit data — h_data_plot","title":"Helper function to tidy survival fit data — h_data_plot","text":"Convert survival fit data data frame designed plotting within g_km. starts broom::tidy() result, : Post-processes strata column factor. Extends stratum additional first row time 0 probability 1 downstream plot lines start coordinates. Adds censor column. Filters rows max_time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"h_data_plot(fit_km, armval = \"All\", max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to tidy survival fit data — h_data_plot","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to tidy survival fit data — h_data_plot","text":"tibble columns time, n.risk, n.event, n.censor, estimate, std.error, conf.high, conf.low, strata, censor.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_data_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"library(dplyr) library(survival)  # Test with multiple arms tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot() #> # A tibble: 203 × 10 #>     time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>    <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <fct>  #>  1   0       70       0        0    1        0          1        1     ARM A  #>  2  10.4     69       1        0    0.986    0.0146     1        0.958 ARM A  #>  3  20.5     68       1        0    0.971    0.0208     1        0.932 ARM A  #>  4  21.5     67       1        0    0.957    0.0257     1        0.910 ARM A  #>  5  25.3     66       0        1    0.957    0.0257     1        0.910 ARM A  #>  6  48.1     65       1        0    0.942    0.0300     0.999    0.888 ARM A  #>  7  66.6     64       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  8  73.9     63       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  9  78.9     62       0        1    0.942    0.0300     0.999    0.888 ARM A  #> 10  90.3     61       1        0    0.926    0.0342     0.991    0.866 ARM A  #> # ℹ 193 more rows #> # ℹ 1 more variable: censor <dbl>  # Test with single arm tern_ex_adtte %>%   filter(PARAMCD == \"OS\", ARMCD == \"ARM B\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot(armval = \"ARM B\") #> # A tibble: 74 × 10 #>      time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>     <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <chr>  #>  1   0        74       0        0    1        0          1        1     ARM B  #>  2   2.17     73       1        0    0.986    0.0138     1        0.960 ARM B  #>  3  16.9      72       1        0    0.973    0.0196     1        0.936 ARM B  #>  4  22.6      71       1        0    0.959    0.0242     1        0.914 ARM B  #>  5  26.3      70       1        0    0.945    0.0282     0.999    0.894 ARM B  #>  6  57.5      69       1        0    0.932    0.0317     0.991    0.875 ARM B  #>  7  80.0      68       1        0    0.918    0.0350     0.983    0.857 ARM B  #>  8  81.6      67       1        0    0.904    0.0381     0.974    0.839 ARM B  #>  9  88.6      66       1        0    0.890    0.0411     0.965    0.822 ARM B  #> 10 102.       65       1        0    0.877    0.0439     0.955    0.804 ARM B  #> # ℹ 64 more rows #> # ℹ 1 more variable: censor <dbl>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot decomposition — h_decompose_gg","title":"ggplot decomposition — h_decompose_gg","text":"elements composing ggplot extracted organized list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot decomposition — h_decompose_gg","text":"","code":"h_decompose_gg(gg)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot decomposition — h_decompose_gg","text":"gg (ggplot) graphic decompose.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot decomposition — h_decompose_gg","text":"named list elements: panel: panel. yaxis: y-axis. xaxis: x-axis. xlab: x-axis label. ylab: y-axis label. guide: legend.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_decompose_gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ggplot decomposition — h_decompose_gg","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   yval = \"Survival\",   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\",   footnotes = \"ff\" ) #> Warning: `h_ggkm()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  g_el <- h_decompose_gg(gg) #> Warning: `h_decompose_gg()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"red\", fill = \"gray85\", lwd = 5)) grid::grid.draw(g_el$panel)   grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"royalblue\", fill = \"gray85\", lwd = 5)) grid::grid.draw(with(g_el, cbind(ylab, yaxis)))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"h_format_row(x, format, labels = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"x (named list) list numerical values formatted optionally labeled. Elements x must numeric vectors. format (named character NULL) format patterns x. Names format must match names x. parameter passed directly rtables::format_rcell function format parameter. labels (named character NULL) optional labels x. Names labels must match names x. label specified element x, function tries use label names (order) attribute element (depending one exists NULL NA NaN). none attributes attached given element x, label automatically generated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"single row data.frame object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_format_row.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"mean_ci <- c(48, 51) x <- list(mean = 50, mean_ci = mean_ci) format <- c(mean = \"xx.x\", mean_ci = \"(xx.xx, xx.xx)\") labels <- c(mean = \"My Mean\") h_format_row(x, format, labels) #>   My Mean             V1 #> 1    50.0 (48.00, 51.00)  attr(mean_ci, \"label\") <- \"Mean 95% CI\" x <- list(mean = 50, mean_ci = mean_ci) h_format_row(x, format, labels) #>   My Mean    Mean 95% CI #> 1    50.0 (48.00, 51.00)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create simple line plot over time — h_g_ipp","title":"Helper function to create simple line plot over time — h_g_ipp","text":"Function generates simple line plot displaying parameter trends time.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"h_g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var,   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create simple line plot over time — h_g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create simple line plot over time — h_g_ipp","text":"ggplot line plot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"library(dplyr) library(nestcolor)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  p <- h_g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   id_var = \"USUBJID\",   ylab = \"SGOT/ALT (U/L)\",   add_baseline_hline = TRUE ) p"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a KM plot — h_ggkm","title":"Helper function to create a KM plot — h_ggkm","text":"Draw Kaplan-Meier plot using ggplot2.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"h_ggkm(   data,   xticks = NULL,   yval = \"Survival\",   censor_show,   xlab,   ylab,   ylim = NULL,   title,   footnotes = NULL,   max_time = NULL,   lwd = 1,   lty = NULL,   pch = 3,   size = 2,   col = NULL,   ci_ribbon = FALSE,   ggtheme = nestcolor::theme_nest() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a KM plot — h_ggkm","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. censor_show (flag) whether show censored observations. xlab (string) x-axis label. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. col (character) lines colors. Length vector equal number strata survival::survfit(). ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a KM plot — h_ggkm","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ggkm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"# \\donttest{ library(dplyr) library(survival)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks,   xlab = \"Days\",   yval = \"Survival\",   ylab = \"Survival Probability\",   title = \"Survival\" ) gg  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Poisson models — h_glm_count","title":"Helper functions for Poisson models — h_glm_count","text":"Helper functions returns results stats::glm() Poisson Quasi-Poisson distributions needed (see family parameter), MASS::glm.nb() Negative Binomial distributions. Link function GLM log.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Poisson models — h_glm_count","text":"","code":"h_glm_count(.var, .df_row, variables, distribution, weights)  h_glm_poisson(.var, .df_row, variables, weights)  h_glm_quasipoisson(.var, .df_row, variables, weights)  h_glm_negbin(.var, .df_row, variables, weights)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Poisson models — h_glm_count","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count() returns results selected model. h_glm_poisson() returns results Poisson model. h_glm_quasipoisson() returns results Quasi-Poisson model. h_glm_negbin() returns results negative binomial model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count(): Helper function return results selected model (Poisson, Quasi-Poisson, negative binomial). h_glm_poisson(): Helper function return results Poisson model. h_glm_quasipoisson(): Helper function return results Quasi-Poisson model. h_glm_negbin(): Helper function return results negative binomial model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create Cox-PH grobs — h_grob_coxph","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"Grob rtable output h_tbl_coxph_pairwise()","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"h_grob_coxph(   ...,   x = 0,   y = 0,   width = grid::unit(0.4, \"npc\"),   ttheme = gridExtra::ttheme_default(padding = grid::unit(c(1, 0.5), \"lines\"), core =     list(bg_params = list(fill = c(\"grey95\", \"grey90\"), alpha = 0.5))) )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"... arguments pass h_tbl_coxph_pairwise(). x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"grob table containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_coxph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) tbl_grob <- h_grob_coxph(   df = data,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\"),   control_coxph_pw = control_coxph(conf_level = 0.9), x = 0.5, y = 0.5 ) #> Warning: `h_grob_coxph()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.draw(tbl_grob)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create survival estimation grobs — h_grob_median_surv","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"survival fit transformed grob containing table groups rows characterized N, median 95% confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"h_grob_median_surv(   fit_km,   armval = \"All\",   x = 0.9,   y = 0.9,   width = grid::unit(0.3, \"npc\"),   ttheme = gridExtra::ttheme_default() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"grob table containing statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_grob_median_surv() %>%   grid::grid.draw() #> Warning: `h_grob_median_surv()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"Two graphical objects obtained, one corresponding row labeling second table numbers patients risk. title = TRUE, third object corresponding table title also obtained.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"data (data.frame) survival data pre-processed h_data_plot. annot_tbl (data.frame) annotation prepared survival::summary.survfit() includes number patients risk given time points. xlim (numeric(1)) maximum value x-axis (used ensure risk table aligns KM graph). title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"named list two gTree objects title = FALSE: at_risk label, three gTree objects title = TRUE: at_risk, label, title.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_tbl_at_risk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)  data_plot <- h_data_plot(fit_km = fit_km)  xticks <- h_xticks(data = data_plot)  gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" )  # The annotation table reports the patient at risk for a given strata and # times (`xticks`). annot_tbl <- summary(fit_km, times = xticks) if (is.null(fit_km$strata)) {   annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = \"All\")) } else {   strata_lst <- strsplit(sub(\"=\", \"equals\", levels(annot_tbl$strata)), \"equals\")   levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]   annot_tbl <- data.frame(     n.risk = annot_tbl$n.risk,     time = annot_tbl$time,     strata = annot_tbl$strata   ) }  # The annotation table is transformed into a grob. tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks)) #> Warning: `h_grob_tbl_at_risk()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # For the representation, the layout is estimated for which the decomposition # of the graphic element is necessary. g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") #> Warning: `h_km_layout()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  grid::grid.newpage() pushViewport(viewport(layout = lyt, height = .95, width = .95)) grid.rect(gp = grid::gpar(lty = 1, col = \"purple\", fill = \"gray85\", lwd = 1)) pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 2)) grid.rect(gp = grid::gpar(lty = 1, col = \"orange\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$at_risk) popViewport() pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 1)) grid.rect(gp = grid::gpar(lty = 1, col = \"green3\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$label)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"Build y-axis annotation decomposed ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"h_grob_y_annot(ylab, yaxis)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"ylab (gtable) y-lab graphical object derived ggplot. yaxis (gtable) y-axis graphical object derived ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"gTree object containing y-axis annotation ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_grob_y_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"title\", footnotes = \"footnotes\", yval = \"Survival\" )  g_el <- h_decompose_gg(gg)  grid::grid.newpage() pvp <- grid::plotViewport(margins = c(5, 4, 2, 20)) pushViewport(pvp) grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis)) #> Warning: `h_grob_y_annot()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid.rect(gp = grid::gpar(lty = 1, col = \"gray35\", fill = NA))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate(person_years, n_events, control = control_incidence_rate())  h_incidence_rate_normal(person_years, n_events, alpha = 0.05)  h_incidence_rate_normal_log(person_years, n_events, alpha = 0.05)  h_incidence_rate_exact(person_years, n_events, alpha = 0.05)  h_incidence_rate_byar(person_years, n_events, alpha = 0.05)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for incidence rate — h_incidence_rate","text":"person_years (numeric(1)) total person-years risk. n_events (integer(1)) number events observed. control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level: (proportion) confidence level estimated incidence rate. conf_type: (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit: (string)day, week, month, year (default) indicating time unit data input. num_pt_year: (numeric) time unit desired output (person-years). alpha (numeric(1)) two-sided alpha-level confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for incidence rate — h_incidence_rate","text":"Estimated incidence rate, rate, associated confidence interval, rate_ci.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for incidence rate — h_incidence_rate","text":"h_incidence_rate(): Helper function estimate incidence rate associated confidence interval. h_incidence_rate_normal(): Helper function estimate incidence rate associated confidence interval based normal approximation incidence rate. Unit one person-year. h_incidence_rate_normal_log(): Helper function estimate incidence rate associated confidence interval based normal approximation logarithm incidence rate. Unit one person-year. h_incidence_rate_exact(): Helper function estimate incidence rate associated exact confidence interval. Unit one person-year. h_incidence_rate_byar(): Helper function estimate incidence rate associated Byar's confidence interval. Unit one person-year.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate_normal(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] -0.003859038  0.023859038 #>   h_incidence_rate_normal_log(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.002500977 0.039984382 #>   h_incidence_rate_exact(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001211046 0.036123438 #>   h_incidence_rate_byar(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001994207 0.032054171 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare a KM layout — h_km_layout","title":"Helper function to prepare a KM layout — h_km_layout","text":"Prepares (5 rows) x (2 cols) layout Kaplan-Meier curve.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"h_km_layout(   data,   g_el,   title,   footnotes,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare a KM layout — h_km_layout","text":"data (data.frame) survival data pre-processed h_data_plot. g_el (list gtable) list obtained h_decompose_gg(). title (string) plot title. footnotes (string) plot footnotes. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare a KM layout — h_km_layout","text":"grid layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function to prepare a KM layout — h_km_layout","text":"layout corresponds grid two columns five rows unequal dimensions. dimension fixed, curve flexible accommodate remaining free space. left column gets annotation ggplot (y-axis) names strata patient risk tabulation. main constraint width columns must allow writing strata name. right column receive ggplot, legend, x-axis patient risk table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_km_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" ) g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") grid.show.layout(lyt)  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for multivariate logistic regression — h_logistic_regression","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Helper functions used calculations logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"h_get_interaction_vars(fit_glm)  h_interaction_coef_name(   interaction_vars,   first_var_with_level,   second_var_with_level )  h_or_cat_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   conf_level = 0.95 )  h_or_cont_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_or_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_simple_term_labels(terms, table)  h_interaction_term_labels(terms1, terms2, table, any = FALSE)  h_glm_simple_term_extract(x, fit_glm)  h_glm_interaction_extract(x, fit_glm)  h_glm_inter_term_extract(odds_ratio_var, interaction_var, fit_glm, ...)  h_logistic_simple_terms(x, fit_glm, conf_level = 0.95)  h_logistic_inter_terms(x, fit_glm, conf_level = 0.95, at = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"fit_glm (glm) logistic regression model fitted stats::glm() \"binomial\" family. Limited functionality also available conditional logistic regression models fitted survival::clogit(), currently used extract_rsp_biomarkers(). interaction_vars (character(2)) interaction variable names. first_var_with_level (character(2)) first variable name interaction level. second_var_with_level (character(2)) second variable name interaction level. odds_ratio_var (string) odds ratio variable. interaction_var (string) interaction variable. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. terms (character) simple terms. table (table) table containing numbers terms. terms1 (character) terms first dimension (rows). terms2 (character) terms second dimension (rows). (flag) whether term1 term2 can fulfilled count number patients. case can scalar (strings). x (character) variable interaction term fit_glm (depending helper function used). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Vector names interaction variables. Name coefficient. Odds ratio. Odds ratio. Odds ratio. Term labels containing numbers patients. Term labels containing numbers patients. Tabulated main effect results logistic regression model. Tabulated interaction term results logistic regression model. data.frame tabulated interaction term results logistic regression model. Tabulated statistics given variable(s) logistic regression model. Tabulated statistics given variable(s) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"h_get_interaction_vars(): Helper function extract interaction variable names fitted model assuming one interaction term. h_interaction_coef_name(): Helper function get right coefficient name interaction variable names given levels. main value order first second variable checked interaction_vars input. h_or_cat_interaction(): Helper function calculate odds ratio estimates case odds ratio interaction variable categorical. h_or_cont_interaction(): Helper function calculate odds ratio estimates case either odds ratio interaction variable continuous. h_or_interaction(): Helper function calculate odds ratio estimates case interaction. wrapper h_or_cont_interaction() h_or_cat_interaction(). h_simple_term_labels(): Helper function construct term labels simple terms table numbers patients. h_interaction_term_labels(): Helper function construct term labels interaction terms table numbers patients. h_glm_simple_term_extract(): Helper function tabulate main effect results (conditional) logistic regression model. h_glm_interaction_extract(): Helper function tabulate interaction term results logistic regression model. h_glm_inter_term_extract(): Helper function tabulate interaction results logistic regression model. basically wrapper h_or_interaction() h_glm_simple_term_extract() puts results right data frame format. h_logistic_simple_terms(): Helper function tabulate results including odds ratios confidence intervals simple terms. h_logistic_inter_terms(): Helper function tabulate results including odds ratios confidence intervals interaction terms.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"provide function case variables continuous arise table, treatment arm variable always involved categorical.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_logistic_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  h_glm_simple_term_extract(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary #> 1               FALSE            TRUE h_glm_simple_term_extract(\"ARMCD\", mod1) #>   variable   variable_label  term              term_label interaction #> 1    ARMCD Planned Arm Code ARM A Reference ARM A, n = 64             #> 2    ARMCD Planned Arm Code ARM B           ARM B, n = 68             #> 3    ARMCD Planned Arm Code ARM C           ARM C, n = 52             #>   interaction_label reference reference_label  estimate std_error df    pvalue #> 1                                                                  2 0.3004308 #> 2                                             -1.774769  1.144405  1 0.1209443 #> 3                                               17.1922  3626.588  1 0.9962176 #>   is_variable_summary is_term_summary #> 1                TRUE           FALSE #> 2               FALSE            TRUE #> 3               FALSE            TRUE  h_glm_interaction_extract(\"ARMCD:AGE\", mod2) #>    variable                        variable_label  term              term_label #> 1 ARMCD:AGE Interaction of Planned Arm Code * Age ARM A Reference ARM A, n = 64 #> 2 ARMCD:AGE Interaction of Planned Arm Code * Age ARM B           ARM B, n = 68 #> 3 ARMCD:AGE Interaction of Planned Arm Code * Age ARM C           ARM C, n = 52 #>   interaction interaction_label reference reference_label   estimate std_error #> 1                                                                              #> 2                                                          0.3081205 0.2062392 #> 3                                                         0.02948826  548.5923 #>   df    pvalue is_variable_summary is_term_summary #> 1  2 0.3275837                TRUE           FALSE #> 2  1 0.1351767               FALSE            TRUE #> 3  1 0.9999571               FALSE            TRUE  h_glm_inter_term_extract(\"AGE\", \"ARMCD\", mod2) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #> 2      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 3      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 4      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #>   reference reference_label    estimate std_error odds_ratio       lcl      ucl #> 1                           -0.03873898 0.1514322         NA        NA       NA #> 2     ARM A           ARM A          NA        NA  0.9620018 0.7149514 1.294420 #> 3     ARM B           ARM B          NA        NA  1.3091545 1.0021802 1.710157 #> 4     ARM C           ARM C          NA        NA  0.9907919 0.0000000      Inf #>   df   pvalue is_variable_summary is_term_summary is_reference_summary #> 1  1 0.798092               FALSE            TRUE                FALSE #> 2 NA       NA               FALSE           FALSE                 TRUE #> 3 NA       NA               FALSE           FALSE                 TRUE #> 4 NA       NA               FALSE           FALSE                 TRUE  h_logistic_simple_terms(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary odds_ratio       lcl      ucl #> 1               FALSE            TRUE   1.185093 0.9832935 1.428308 #>                     ci #> 1 0.9832935, 1.4283084  h_logistic_inter_terms(c(\"RACE\", \"AGE\", \"ARMCD\", \"AGE:ARMCD\"), mod2) #>        variable                        variable_label                      term #> 1          RACE                                  Race                     ASIAN #> 2          RACE                                  Race BLACK OR AFRICAN AMERICAN #> 3          RACE                                  Race                     WHITE #> 13        ARMCD                      Planned Arm Code                     ARM A #> 23        ARMCD                      Planned Arm Code                     ARM B #> ARM B     ARMCD                      Planned Arm Code                     ARM B #> 33        ARMCD                      Planned Arm Code                     ARM C #> ARM C     ARMCD                      Planned Arm Code                     ARM C #> 11          AGE                                   Age                       AGE #> 21          AGE                                   Age                       AGE #> 31          AGE                                   Age                       AGE #> 4           AGE                                   Age                       AGE #> 12    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM A #> 22    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM B #> 32    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM C #>                              term_label interaction interaction_label reference #> 1              Reference ASIAN, n = 110                                         #> 2     BLACK OR AFRICAN AMERICAN, n = 40                                         #> 3                         WHITE, n = 34                                         #> 13              Reference ARM A, n = 64                                         #> 23                        ARM B, n = 68                                         #> ARM B                     ARM B, n = 68         AGE               Age        35 #> 33                        ARM C, n = 52                                         #> ARM C                     ARM C, n = 52         AGE               Age        35 #> 11                                  Age                                         #> 21                                  Age       ARMCD  Planned Arm Code     ARM A #> 31                                  Age       ARMCD  Planned Arm Code     ARM B #> 4                                   Age       ARMCD  Planned Arm Code     ARM C #> 12              Reference ARM A, n = 64                                         #> 22                        ARM B, n = 68                                         #> 32                        ARM C, n = 52                                         #>       reference_label    estimate std_error df     pvalue odds_ratio        lcl #> 1                                            2  0.9361139                       #> 2                        18.15018  3944.701  1  0.9963288   76299564          0 #> 3                      -0.3727152  1.025808  1  0.7163522  0.6888614 0.09224926 #> 13                                           2   0.253914         NA         NA #> 23                      -11.52715   6.96188  1 0.09777185         NA         NA #> ARM B              35          NA        NA NA         NA  0.4757148 0.03361147 #> 33                       16.33327  20278.39  1  0.9993573         NA         NA #> ARM C              35          NA        NA NA         NA   34808099          0 #> 11                    -0.03873898 0.1514322  1   0.798092         NA         NA #> 21              ARM A          NA        NA NA         NA  0.9620018  0.7149514 #> 31              ARM B          NA        NA NA         NA   1.309155    1.00218 #> 4               ARM C          NA        NA NA         NA  0.9907919          0 #> 12                                          NA         NA         NA         NA #> 22                      0.3081205 0.2062392  1  0.1351767         NA         NA #> 32                     0.02948826  548.5923  1  0.9999571         NA         NA #>            ucl is_variable_summary is_term_summary is_reference_summary #> 1                             TRUE           FALSE                FALSE #> 2          Inf               FALSE            TRUE                FALSE #> 3     5.143998               FALSE            TRUE                FALSE #> 13          NA                TRUE           FALSE                FALSE #> 23          NA               FALSE            TRUE                FALSE #> ARM B 6.732956               FALSE           FALSE                 TRUE #> 33          NA               FALSE            TRUE                FALSE #> ARM C      Inf               FALSE           FALSE                 TRUE #> 11          NA               FALSE            TRUE                FALSE #> 21     1.29442               FALSE           FALSE                 TRUE #> 31    1.710157               FALSE           FALSE                 TRUE #> 4          Inf               FALSE           FALSE                 TRUE #> 12          NA                TRUE           FALSE                FALSE #> 22          NA               FALSE            TRUE                FALSE #> 32          NA               FALSE            TRUE                FALSE #>                           ci #> 1                            #> 2                     0, Inf #> 3     0.09224926, 5.14399810 #> 13                    NA, NA #> 23                    NA, NA #> ARM B 0.03361147, 6.73295611 #> 33                    NA, NA #> ARM C                 0, Inf #> 11                    NA, NA #> 21      0.7149514, 1.2944200 #> 31        1.002180, 1.710157 #> 4                     0, Inf #> 12                    NA, NA #> 22                    NA, NA #> 32                    NA, NA"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"Helper function create map data frame input dataset, can used argument trim_levels_to_map split function. Based different method, map constructed differently.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"h_map_for_count_abnormal(   df,   variables = list(anl = \"ANRIND\", split_rows = c(\"PARAM\"), range_low = \"ANRLO\",     range_high = \"ANRHI\"),   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   method = c(\"default\", \"range\"),   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"df (data.frame) data set containing analysis variables. variables (named list string) list additional analysis variables. abnormal (named list) identifying abnormal range level(s) df. Based levels abnormality input dataset, can something like list(Low = \"LOW LOW\", High = \"HIGH HIGH\") abnormal = list(Low = \"LOW\", High = \"HIGH\")) method (string) indicates returned map constructed. Can \"default\" \"range\". na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"map data.frame.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"method \"default\", returned map abnormal directions observed df, records normal values excluded avoid error creating layout. method \"range\", returned map based rule least one observation low range > 0 low direction least one observation high range missing high direction.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_map_for_count_abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"adlb <- df_explicit_na(tern_ex_adlb)  h_map_for_count_abnormal(   df = adlb,   variables = list(anl = \"ANRIND\", split_rows = c(\"LBCAT\", \"PARAM\")),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"default\",   na_str = \"<Missing>\" ) #>        LBCAT                                PARAM ANRIND #> 1  CHEMISTRY Alanine Aminotransferase Measurement    LOW #> 4  CHEMISTRY Alanine Aminotransferase Measurement   HIGH #> 7  CHEMISTRY Alanine Aminotransferase Measurement NORMAL #> 2  CHEMISTRY       C-Reactive Protein Measurement    LOW #> 3  CHEMISTRY       C-Reactive Protein Measurement   HIGH #> 8  CHEMISTRY       C-Reactive Protein Measurement NORMAL #> 5 IMMUNOLOGY         Immunoglobulin A Measurement    LOW #> 6 IMMUNOLOGY         Immunoglobulin A Measurement   HIGH #> 9 IMMUNOLOGY         Immunoglobulin A Measurement NORMAL  df <- data.frame(   USUBJID = c(rep(\"1\", 4), rep(\"2\", 4), rep(\"3\", 4)),   AVISIT = c(     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2)   ),   PARAM = rep(c(\"ALT\", \"CPR\"), 6),   ANRIND = c(     \"NORMAL\", \"NORMAL\", \"LOW\",     \"HIGH\", \"LOW\", \"LOW\", \"HIGH\", \"HIGH\", rep(\"NORMAL\", 4)   ),   ANRLO = rep(5, 12),   ANRHI = rep(20, 12) ) df$ANRIND <- factor(df$ANRIND, levels = c(\"LOW\", \"HIGH\", \"NORMAL\")) h_map_for_count_abnormal(   df = df,   variables = list(     anl = \"ANRIND\",     split_rows = c(\"PARAM\"),     range_low = \"ANRLO\",     range_high = \"ANRHI\"   ),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"range\",   na_str = \"<Missing>\" ) #>   PARAM ANRIND #> 1   ALT    LOW #> 3   ALT   HIGH #> 5   ALT NORMAL #> 2   CPR    LOW #> 4   CPR   HIGH #> 6   CPR NORMAL"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for odds ratio estimation — h_odds_ratio","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"Functions calculate odds ratios estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"or_glm(data, conf_level)  or_clogit(data, conf_level, method = \"exact\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"data (data.frame) data frame containing least variables rsp grp, optionally strata or_clogit(). conf_level (proportion) confidence level interval. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"named list elements or_ci n_tot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"or_glm(): Estimates odds ratio based stats::glm(). Note must exactly 2 groups data specified grp variable. or_clogit(): Estimates odds ratio based survival::clogit(). done whole data set including groups, since results pairwise comparisons groups.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"# Data with 2 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1)),   grp = letters[c(1, 1, 1, 2, 2, 2, 1, 2)],   strata = letters[c(1, 2, 1, 2, 2, 2, 1, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on glm. or_glm(data, conf_level = 0.95) #> $or_ci #>        est        lcl        ucl  #> 0.33333333 0.01669735 6.65441589  #>  #> $n_tot #> n_tot  #>     8  #>   # Data with 3 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0)),   grp = letters[c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3)],   strata = LETTERS[c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on stratified estimation by conditional logistic regression. or_clogit(data, conf_level = 0.95) #> $or_ci #> $or_ci$b #>        est        lcl        ucl  #> 0.28814553 0.02981009 2.78522598  #>  #> $or_ci$c #>       est       lcl       ucl  #> 0.5367919 0.0673365 4.2791881  #>  #>  #> $n_tot #> n_tot  #>    20  #>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"h_pkparam_sort(pk_data, key_var = \"PARAMCD\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pk_data (data.frame) pharmacokinetic data frame. key_var (string) key variable used merge pk_data metadata created d_pkparam().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pharmacokinetic data.frame sorted PARAM variable.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_pkparam_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"library(dplyr)  adpp <- tern_ex_adpp %>% mutate(PKPARAM = factor(paste0(PARAM, \" (\", AVALU, \")\"))) pk_ordered_data <- h_pkparam_sort(adpp)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to return the estimated means using predicted probabilities — h_ppmeans","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"arm level, predicted mean rate calculated using fitted model object, newdata set result stats::model.frame, reconstructed data original data, depending object formula (coming fit). confidence interval derived using conf_level parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"","code":"h_ppmeans(obj, .df_row, arm, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"obj (glm.fit) fitted model object used derive mean rate estimates treatment arm. .df_row (data.frame) dataset includes variables called .var variables. arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. conf_level (proportion) value used derive confidence interval rate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_ppmeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"h_ppmeans() returns estimated means.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"prop_diff_wald(rsp, grp, conf_level = 0.95, correct = FALSE)  prop_diff_ha(rsp, grp, conf_level)  prop_diff_nc(rsp, grp, conf_level, correct = FALSE)  prop_diff_cmh(rsp, grp, strata, conf_level = 0.95)  prop_diff_strat_nc(   rsp,   grp,   strata,   weights_method = c(\"cmh\", \"wilson_h\"),   conf_level = 0.95,   correct = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test(). strata (factor) variable one level per stratum length rsp. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"named list elements diff (proportion difference) diff_ci (proportion difference confidence interval).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"prop_diff_wald(): Wald interval follows usual textbook definition single proportion confidence interval using normal approximation. possible include continuity correction Wald's interval. prop_diff_ha(): Anderson-Hauck confidence interval. prop_diff_nc(): Newcombe confidence interval. based Wilson score confidence interval single binomial proportion. prop_diff_cmh(): Calculates weighted difference. defined difference response rates experimental treatment group control treatment group, adjusted stratification factors applying Cochran-Mantel-Haenszel (CMH) weights. CMH chi-squared test, use stats::mantelhaen.test(). prop_diff_strat_nc(): Calculates stratified Newcombe confidence interval difference response rates experimental treatment group control treatment group, adjusted stratification factors. implementation follows closely one proposed Yan2010-jt;textualtern. Weights can estimated heuristic proposed prop_strat_wilson() CMH-derived weights (see prop_diff_cmh()).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"# Wald confidence interval set.seed(2) rsp <- sample(c(TRUE, FALSE), replace = TRUE, size = 20) grp <- factor(c(rep(\"A\", 10), rep(\"B\", 10)))  prop_diff_wald(rsp = rsp, grp = grp, conf_level = 0.95, correct = FALSE) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.4382613  0.4382613 #>   # Anderson-Hauck confidence interval ## \"Mid\" case: 3/4 respond in group A, 1/2 respond in group B. rsp <- c(TRUE, FALSE, FALSE, TRUE, TRUE, TRUE) grp <- factor(c(\"A\", \"B\", \"A\", \"B\", \"A\", \"A\"), levels = c(\"B\", \"A\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.90) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] -0.9195011  1.0000000 #>   ## Edge case: Same proportion of response in A and B. rsp <- c(TRUE, FALSE, TRUE, FALSE) grp <- factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.6) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.8451161  0.8451161 #>   # Newcombe confidence interval  set.seed(1) rsp <- c(   sample(c(TRUE, FALSE), size = 40, prob = c(3 / 4, 1 / 4), replace = TRUE),   sample(c(TRUE, FALSE), size = 40, prob = c(1 / 2, 1 / 2), replace = TRUE) ) grp <- factor(rep(c(\"A\", \"B\"), each = 40), levels = c(\"B\", \"A\")) table(rsp, grp) #>        grp #> rsp      B  A #>   FALSE 20 10 #>   TRUE  20 30  prop_diff_nc(rsp = rsp, grp = grp, conf_level = 0.9) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] 0.07193388 0.40725819 #>   # Cochran-Mantel-Haenszel confidence interval  set.seed(2) rsp <- sample(c(TRUE, FALSE), 100, TRUE) grp <- sample(c(\"Placebo\", \"Treatment\"), 100, TRUE) grp <- factor(grp, levels = c(\"Placebo\", \"Treatment\")) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_cmh(   rsp = rsp, grp = grp, strata = interaction(strata_data),   conf_level = 0.90 ) #> $prop #>   Placebo Treatment  #> 0.5331117 0.3954251  #>  #> $prop_ci #> $prop_ci$Placebo #> [1] 0.4306536 0.6355698 #>  #> $prop_ci$Treatment #> [1] 0.2890735 0.5017768 #>  #>  #> $diff #> [1] -0.1376866 #>  #> $diff_ci #> [1] -0.285363076  0.009989872 #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.1148388 0.2131696 0.1148388 0.2131696 0.1767914 0.1671918  #>  #> $n1 #> a.x b.x a.y b.y a.z b.z  #>   4  11   8  11  13  11  #>  #> $n2 #> a.x b.x a.y b.y a.z b.z  #>   8   9   4   9   6   6  #>   # Stratified Newcombe confidence interval  set.seed(2) data_set <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   \"grp\" = sample(c(\"Placebo\", \"Treatment\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"cmh\",   conf_level = 0.90 ) #> $diff #> [1] -0.05777672 #>  #> $diff_ci #>      lower      upper  #> -0.2236537  0.1119331  #>   prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"wilson_h\",   conf_level = 0.90 ) #> $diff #> [1] -0.07771884 #>  #> $diff_ci #>      lower      upper  #> -0.2540844  0.1027720  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions to test proportion differences — h_prop_diff_test","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"Helper functions implement various tests difference two proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"","code":"prop_chisq(tbl)  prop_cmh(ary)  prop_schouten(tbl)  prop_fisher(tbl)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"tbl (matrix) matrix two groups rows binary response (TRUE/FALSE) columns. ary (array, 3 dimensions) array two groups rows, binary response (TRUE/FALSE) columns, strata third dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"prop_chisq(): Performs Chi-Squared test. Internally calls stats::prop.test(). prop_cmh(): Performs stratified Cochran-Mantel-Haenszel test. Internally calls stats::mantelhaen.test(). Note strata less two observations automatically discarded. prop_schouten(): Performs Chi-Squared test Schouten correction. prop_fisher(): Performs Fisher's exact test. Internally calls stats::fisher.test().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for calculating proportion confidence intervals — h_proportions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Functions calculate different proportion confidence intervals use estimate_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"prop_wilson(rsp, conf_level, correct = FALSE)  prop_strat_wilson(   rsp,   strata,   weights = NULL,   conf_level = 0.95,   max_iterations = NULL,   correct = FALSE )  prop_clopper_pearson(rsp, conf_level)  prop_wald(rsp, conf_level, correct = FALSE)  prop_agresti_coull(rsp, conf_level)  prop_jeffreys(rsp, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"rsp (logical) vector indicating whether subject responder . conf_level (proportion) confidence level interval. correct (flag) whether apply continuity correction. strata (factor) variable one level per stratum length rsp. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Confidence interval proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"prop_wilson(): Calculates Wilson interval calling stats::prop.test(). Also referred Wilson score interval. prop_strat_wilson(): Calculates stratified Wilson confidence interval unequal proportions described Yan2010-jt;textualtern prop_clopper_pearson(): Calculates Clopper-Pearson interval calling stats::binom.test(). Also referred exact method. prop_wald(): Calculates Wald interval following usual textbook definition single proportion confidence interval using normal approximation. prop_agresti_coull(): Calculates Agresti-Coull interval. Constructed (95% CI) adding two successes two failures data using Wald formula construct CI. prop_jeffreys(): Calculates Jeffreys interval, equal-tailed interval based non-informative Jeffreys prior binomial proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_proportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"rsp <- c(   TRUE, TRUE, TRUE, TRUE, TRUE,   FALSE, FALSE, FALSE, FALSE, FALSE ) prop_wilson(rsp, conf_level = 0.9) #> [1] 0.2692718 0.7307282  # Stratified Wilson confidence interval with unequal probabilities  set.seed(1) rsp <- sample(c(TRUE, FALSE), 100, TRUE) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE ) strata <- interaction(strata_data) n_strata <- ncol(table(rsp, strata)) # Number of strata  prop_strat_wilson(   rsp = rsp, strata = strata,   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4072891 0.5647887  #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.2074199 0.1776464 0.1915610 0.1604678 0.1351096 0.1277952  #>   # Not automatic setting of weights prop_strat_wilson(   rsp = rsp, strata = strata,   weights = rep(1 / n_strata, n_strata),   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4190436 0.5789733  #>   prop_clopper_pearson(rsp, conf_level = .95) #> [1] 0.3886442 0.5919637  prop_wald(rsp, conf_level = 0.95) #> [1] 0.3920214 0.5879786 prop_wald(rsp, conf_level = 0.95, correct = TRUE) #> [1] 0.3870214 0.5929786  prop_agresti_coull(rsp, conf_level = 0.95) #> [1] 0.3942193 0.5865206  prop_jeffreys(rsp, conf_level = 0.95) #> [1] 0.3934779 0.5870917"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"h_rsp_to_logistic_variables(variables, biomarker)  h_logistic_mult_cont_df(variables, data, control = control_logistic())  h_tab_rsp_one_biomarker(df, vars, na_str = default_na_str(), .indent_mods = 0L)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (named list) controls response definition confidence level produced control_logistic(). df (data.frame) results single biomarker, part returned extract_rsp_biomarkers() (needs couple columns added high-level function relative returned h_logistic_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables() returns named list elements response, arm, covariates, strata. h_logistic_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_rsp_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables(): helps converting \"response\" function variable list \"logistic regression\" variable list. reason currently inconsistency variable names accepted extract_rsp_subgroups() fit_logistic(). h_logistic_mult_cont_df(): prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates strata. h_tab_rsp_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # This is how the variable list is converted internally. h_rsp_to_logistic_variables(   variables = list(     rsp = \"RSP\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $response #> [1] \"RSP\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_logistic_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp prop        or       lcl #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.82 0.9755036 0.8804862 #> 2       AGE                          Age   200   164 0.82 0.9952416 0.9462617 #>        ucl conf_level      pval     pval_label #> 1 1.080775       0.95 0.6352602 p-value (Wald) #> 2 1.046757       0.95 0.8530389 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = \"STRATA1\"   ),   data = adrs_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\"  h_tab_rsp_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\") ) #>                Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200        164          82.0%          0.98      (0.88, 1.08)       0.6353"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Helper functions tabulate data frame statistics response rate odds ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"h_proportion_df(rsp, arm)  h_proportion_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_odds_ratio_df(rsp, arm, strata_data = NULL, conf_level = 0.95, method = NULL)  h_odds_ratio_subgroups_df(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"rsp (logical) vector indicating whether subject responder . arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df() returns data.frame columns arm, n, n_rsp, prop. h_proportion_subgroups_df() returns data.frame columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. h_odds_ratio_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, optionally pval pval_label. h_odds_ratio_subgroups_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df(): Helper prepare data frame binary responses arm. h_proportion_subgroups_df(): Summarizes proportion binary responses arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_odds_ratio_df(): Helper prepare data frame estimates odds ratio treatment control arm. h_odds_ratio_subgroups_df(): Summarizes estimates odds ratio treatment control arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  h_proportion_df(   c(TRUE, FALSE, FALSE),   arm = factor(c(\"A\", \"A\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n n_rsp prop #> 1   A 2     1  0.5 #> 2   B 1     0  0.0  h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Unstratatified analysis. h_odds_ratio_df(   c(TRUE, FALSE, FALSE, TRUE),   arm = factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n_tot or        lcl      ucl conf_level #> 1         4  1 0.01984252 50.39681       0.95  # Include p-value. h_odds_ratio_df(adrs_f$rsp, adrs_f$ARM, method = \"chisq\") #>   arm n_tot    or      lcl      ucl conf_level       pval #> 1       142 2.714 1.180449 6.239827       0.95 0.01643036 #>                   pval_label #> 1 p-value (Chi-Squared Test)  # Stratatified analysis. h_odds_ratio_df(   rsp = adrs_f$rsp,   arm = adrs_f$ARM,   strata_data = adrs_f[, c(\"STRATA1\", \"STRATA2\")],   method = \"cmh\" ) #>   arm n_tot       or      lcl      ucl conf_level       pval #> 1       142 2.665586 1.146149 6.199324       0.95 0.02019665 #>                               pval_label #> 1 p-value (Cochran-Mantel-Haenszel Test)  # Unstratified analysis. h_odds_ratio_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Stratified analysis. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6655860 1.1461490  6.199324       0.95 All Patients    ALL #> 2        78 7.7065093 1.5817529 37.547132       0.95            F    SEX #> 3        64 0.9572284 0.2990954  3.063525       0.95            M    SEX #> 4        50 3.0323726 0.8833232 10.409875       0.95          LOW BMRKR2 #> 5        49 2.1264996 0.4312008 10.486995       0.95       MEDIUM BMRKR2 #> 6        43 2.5134820 0.4351747 14.517370       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split data frame by subgroups — h_split_by_subgroups","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Split data frame non-nested list subsets.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"h_split_by_subgroups(data, subgroups, groups_lists = list())"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split data frame by subgroups — h_split_by_subgroups","text":"data (data.frame) dataset split. subgroups (character) names factor variables data used create subsets. Unused levels present data dropped. Note order vector determines order downstream table. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split data frame by subgroups — h_split_by_subgroups","text":"list subset data (df) metadata subset (df_labels).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Main functionality prepare data use forest plot layouts.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_by_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"df <- data.frame(   x = c(1:5),   y = factor(c(\"A\", \"B\", \"A\", \"B\", \"A\"), levels = c(\"A\", \"B\", \"C\")),   z = factor(c(\"C\", \"C\", \"D\", \"D\", \"D\"), levels = c(\"D\", \"C\")) ) formatters::var_labels(df) <- paste(\"label for\", names(df))  h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\") ) #> $y.A #> $y.A$df #>   x y z #> 1 1 A C #> 2 3 A D #> 3 5 A D #>  #> $y.A$df_labels #>   subgroup var   var_label #> 1        A   y label for y #>  #>  #> $y.B #> $y.B$df #>   x y z #> 1 2 B C #> 2 4 B D #>  #> $y.B$df_labels #>   subgroup var   var_label #> 1        B   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>   h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\"),   groups_lists = list(     y = list(\"AB\" = c(\"A\", \"B\"), \"C\" = \"C\")   ) ) #> $y.AB #> $y.AB$df #>   x y z #> 1 1 A C #> 2 2 B C #> 3 3 A D #> 4 4 B D #> 5 5 A D #>  #> $y.AB$df_labels #>   subgroup var   var_label #> 1       AB   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Split parameters — h_split_param","title":"Split parameters — h_split_param","text":"divides data vector param groups defined f based specified values. relevant rtables layers distribute parameters .stats ' .formats lists items corresponding specific analysis function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split parameters — h_split_param","text":"","code":"h_split_param(param, value, f)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split parameters — h_split_param","text":"param (vector) parameter split. value (vector) value used split. f (list) reference make split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split parameters — h_split_param","text":"named list element names f, containing elements specified .stats.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_split_param.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split parameters — h_split_param","text":"","code":"f <- list(   surv = c(\"pt_at_risk\", \"event_free_rate\", \"rate_se\", \"rate_ci\"),   surv_diff = c(\"rate_diff\", \"rate_diff_ci\", \"ztest_pval\") )  .stats <- c(\"pt_at_risk\", \"rate_diff\") h_split_param(.stats, .stats, f = f) #> $surv #> [1] \"pt_at_risk\" #>  #> $surv_diff #> [1] \"rate_diff\" #>   # $surv # [1] \"pt_at_risk\" # # $surv_diff # [1] \"rate_diff\"  .formats <- c(\"pt_at_risk\" = \"xx\", \"event_free_rate\" = \"xxx\") h_split_param(.formats, names(.formats), f = f) #> $surv #>      pt_at_risk event_free_rate  #>            \"xx\"           \"xxx\"  #>  #> $surv_diff #> NULL #>   # $surv # pt_at_risk event_free_rate # \"xx\"           \"xxx\" # # $surv_diff # NULL"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"Helper function create new SMQ variable ADAE consists adverse events belonging selected Standardized/Customized queries. new dataset contain records adverse events belonging selected baskets. Remember na_str must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"h_stack_by_baskets(   df,   baskets = grep(\"^(SMQ|CQ).+NAM$\", names(df), value = TRUE),   smq_varlabel = \"Standardized MedDRA Query\",   keys = c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"AEDECOD\", \"AESEQ\"),   aag_summary = NULL,   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"df (data.frame) data set containing analysis variables. baskets (character) variable names selected Standardized/Customized queries. smq_varlabel (string) label new variable created. keys (character) names key variables returned along new variable created. aag_summary (data.frame) containing SMQ baskets levels interest final SMQ variable. useful levels interest observed df dataset. two columns dataset named basket basket_name. na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"data.frame variables keys taken df new variable SMQ containing records belonging baskets selected via baskets argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_stack_by_baskets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"adae <- tern_ex_adae[1:20, ] %>% df_explicit_na() h_stack_by_baskets(df = adae) #> # A tibble: 8 × 6 #>   STUDYID USUBJID               ASTDTM              AEDECOD       AESEQ SMQ      #>   <fct>   <fct>                 <dttm>              <fct>         <int> <fct>    #> 1 AB12345 AB12345-BRA-11-id-8   2021-12-05 02:02:07 dcd D.2.1.5.3     2 D.2.1.5… #> 2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3     2 D.2.1.5… #> 3 AB12345 AB12345-BRA-1-id-171  2022-11-29 12:18:31 dcd C.1.1.1.3     2 C.1.1.1… #> 4 AB12345 AB12345-BRA-1-id-23   2020-07-10 07:32:49 dcd B.2.2.3.1     3 C.1.1.1… #> 5 AB12345 AB12345-BRA-1-id-59   2021-10-10 23:54:46 dcd C.1.1.1.3     4 C.1.1.1… #> 6 AB12345 AB12345-BRA-1-id-9    2021-06-01 14:39:09 dcd C.1.1.1.3     1 C.1.1.1… #> 7 AB12345 AB12345-BRA-11-id-8   2021-12-21 02:02:07 dcd C.1.1.1.3     3 C.1.1.1… #> 8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3     3 C.1.1.1…  aag <- data.frame(   NAMVAR = c(\"CQ01NAM\", \"CQ02NAM\", \"SMQ01NAM\", \"SMQ02NAM\"),   REFNAME = c(     \"D.2.1.5.3/A.1.1.1.1 aesi\", \"X.9.9.9.9/Y.8.8.8.8 aesi\",     \"C.1.1.1.3/B.2.2.3.1 aesi\", \"C.1.1.1.3/B.3.3.3.3 aesi\"   ),   SCOPE = c(\"\", \"\", \"BROAD\", \"BROAD\"),   stringsAsFactors = FALSE )  basket_name <- character(nrow(aag)) cq_pos <- grep(\"^(CQ).+NAM$\", aag$NAMVAR) smq_pos <- grep(\"^(SMQ).+NAM$\", aag$NAMVAR) basket_name[cq_pos] <- aag$REFNAME[cq_pos] basket_name[smq_pos] <- paste0(   aag$REFNAME[smq_pos], \"(\", aag$SCOPE[smq_pos], \")\" )  aag_summary <- data.frame(   basket = aag$NAMVAR,   basket_name = basket_name,   stringsAsFactors = TRUE )  result <- h_stack_by_baskets(df = adae, aag_summary = aag_summary) all(levels(aag_summary$basket_name) %in% levels(result$SMQ)) #> [1] TRUE  h_stack_by_baskets(   df = adae,   aag_summary = NULL,   keys = c(\"STUDYID\", \"USUBJID\", \"AEDECOD\", \"ARM\"),   baskets = \"SMQ01NAM\" ) #> # A tibble: 6 × 5 #>   STUDYID USUBJID               AEDECOD       ARM            SMQ                 #>   <fct>   <fct>                 <fct>         <fct>          <fct>               #> 1 AB12345 AB12345-BRA-1-id-171  dcd C.1.1.1.3 B: Placebo     C.1.1.1.3/B.2.2.3.… #> 2 AB12345 AB12345-BRA-1-id-23   dcd B.2.2.3.1 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 3 AB12345 AB12345-BRA-1-id-59   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 4 AB12345 AB12345-BRA-1-id-9    dcd C.1.1.1.3 C: Combination C.1.1.1.3/B.2.2.3.… #> 5 AB12345 AB12345-BRA-11-id-8   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 6 AB12345 AB12345-BRA-12-id-120 dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.…"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"Helper functions used internally STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"","code":"h_step_window(x, control = control_step())  h_step_trt_effect(data, model, variables, x)  h_step_survival_formula(variables, control = control_step())  h_step_survival_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_coxph() )  h_step_rsp_formula(variables, control = c(control_step(), control_logistic()))  h_step_rsp_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_logistic() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"x (numeric) biomarker value(s) use (without NA). control (named list) output control_step(). data (data.frame) dataset containing variables summarize. model (coxph glm) regression model object. variables (named list string) list additional analysis variables. formula (formula) regression model formula. subset (logical) subset vector.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window() returns list containing window-selection matrix sel interval information matrix interval. h_step_trt_effect() returns vector elements est se. h_step_survival_formula() returns model formula. h_step_survival_est() returns matrix number observations n, events, log hazard ratio estimates loghr, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x. h_step_rsp_formula() returns model formula. h_step_rsp_est() returns matrix number observations n, log odds ratio estimates logor, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_step.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window(): Creates windows STEP, based control settings provided. h_step_trt_effect(): Calculates estimated treatment effect estimate linear predictor scale corresponding standard error STEP model fitted data given variables specification, single biomarker value x. works coxph glm models, .e. calculating log hazard ratio log odds ratio estimates. h_step_survival_formula(): Builds model formula used survival STEP calculations. h_step_survival_est(): Estimates model formula built based variables data given subset control parameters Cox regression. h_step_rsp_formula(): Builds model formula used response STEP calculations. h_step_rsp_est(): Estimates model formula built based variables data given subset control parameters logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"h_surv_to_coxreg_variables(variables, biomarker)  h_coxreg_mult_cont_df(variables, data, control = control_coxreg())  h_tab_surv_one_biomarker(   df,   vars,   time_unit,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (list) list parameters returned helper function control_coxreg(). df (data.frame) results single biomarker, part returned extract_survival_biomarkers() (needs couple columns added high-level function relative returned h_coxreg_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables() returns named list elements time, event, arm, covariates, strata. h_coxreg_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_surv_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables(): Helps converting \"survival\" function variable list \"Cox regression\" variable list. reason currently inconsistency variable names accepted extract_survival_subgroups() fit_coxreg_multivar(). h_coxreg_mult_cont_df(): Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables) optionally subgroups strata. h_tab_surv_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = FALSE)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # This is how the variable list is converted internally. h_surv_to_coxreg_variables(   variables = list(     tte = \"AVAL\",     is_event = \"EVNT\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $time #> [1] \"AVAL\" #>  #> $event #> [1] \"EVNT\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median       hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.000189 #> 2       AGE                          Age   200          141 753.5176 1.008267 #>         lcl      ucl conf_level      pval     pval_label #> 1 0.9511092 1.051802       0.95 0.9941244 p-value (Wald) #> 2 0.9845155 1.032591       0.95 0.4984743 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"REGION1\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\" h_tab_surv_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   time_unit = \"days\" ) #>                Total n   Total Events   Median (days)   Hazard Ratio   95% Wald CI    p-value (Wald) #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200         141            753.5           1.00       (0.95, 1.05)       0.9941"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Helper functions tabulate data frame statistics median survival time hazard ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"h_survtime_df(tte, is_event, arm)  h_survtime_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_coxph_df(tte, is_event, arm, strata_data = NULL, control = control_coxph())  h_coxph_subgroups_df(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"tte (numeric) vector time--event duration values. is_event (flag)TRUE event, FALSE time event censored. arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df() returns data.frame columns arm, n, n_events, median. h_survtime_subgroups_df() returns data.frame columns arm, n, n_events, median, subgroup, var, var_label, row_type. h_coxph_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval pval_label. h_coxph_subgroups_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df(): Helper prepare data frame median survival times arm. h_survtime_subgroups_df(): Summarizes median survival times arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_coxph_df(): Helper prepare data frame estimates treatment hazard ratio. h_coxph_subgroups_df(): Summarizes estimates treatment hazard ratio across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = adtte_labels[[\"ARM\"]], \"SEX\" = adtte_labels[[\"SEX\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Extract median survival time for one group. h_survtime_df(   tte = adtte_f$AVAL,   is_event = adtte_f$is_event,   arm = adtte_f$ARM ) #>          arm  n n_events   median #> 1 B: Placebo 73       57 727.8043 #> 2  A: Drug X 69       44 974.6402  # Extract median survival time for multiple groups. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>           arm  n n_events    median     subgroup    var #> 1  B: Placebo 73       57  727.8043 All Patients    ALL #> 2   A: Drug X 69       44  974.6402 All Patients    ALL #> 3  B: Placebo 40       31  599.1772            F    SEX #> 4   A: Drug X 38       24 1016.2982            F    SEX #> 5  B: Placebo 33       26  888.4916            M    SEX #> 6   A: Drug X 31       20  974.6402            M    SEX #> 7  B: Placebo 24       21  735.4722          LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402          LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352       MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197       MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245         HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Extract hazard ratio for one group. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM) #>   arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for one group with stratification factor. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM, strata_data = adtte_f$STRATA1) #>   arm n_tot n_tot_events        hr       lcl     ucl conf_level       pval #> 1       142          101 0.6646586 0.4399495 1.00414       0.95 0.05089188 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for multiple groups. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis  # Extract hazard ratio for multiple groups with stratification factors. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.6126133 0.3913507 0.9589739       0.95 0.03086774 #> 2        78           55 0.3934024 0.2027682 0.7632630       0.95 0.00469167 #> 3        64           46 0.9501768 0.4730073 1.9087145       0.95 0.88580522 #> 4        50           36 0.7378635 0.3140465 1.7336363       0.95 0.48408079 #> 5        49           31 0.9408062 0.4172095 2.1215148       0.95 0.88305965 #> 6        43           34 0.5125617 0.2125140 1.2362459       0.95 0.13124382 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"Please see h_tab_surv_one_biomarker() h_tab_rsp_one_biomarker(), use function examples. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"","code":"h_tab_one_biomarker(   df,   afuns,   colvars,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"df (data.frame) results single biomarker. afuns (named list function) analysis functions. colvars (named list) named list elements vars (variables tabulate) labels (labels). na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tab_one_biomarker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"rtables table object statistics columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"Create data.frame pairwise stratified unstratified Cox-PH analysis results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"h_tbl_coxph_pairwise(   df,   variables,   ref_group_coxph = NULL,   control_coxph_pw = control_coxph(),   annot_coxph_ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. annot_coxph_ref_lbls (flag) whether reference group explicitly printed labels annot_coxph table. FALSE (default), comparison groups printed annot_coxph table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"data.frame containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  h_tbl_coxph_pairwise(   df = adtte,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARM\"),   control_coxph_pw = control_coxph(conf_level = 0.9) ) #>                  HR       90% CI p-value (log-rank) #> B: Placebo     1.41 (1.01, 1.96)             0.0905 #> C: Combination 1.81 (1.24, 2.64)             0.0086"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for survival estimations — h_tbl_median_surv","title":"Helper function for survival estimations — h_tbl_median_surv","text":"Transform survival fit table groups rows characterized N, median confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"h_tbl_median_surv(fit_km, armval = \"All\")"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for survival estimations — h_tbl_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for survival estimations — h_tbl_median_surv","text":"summary table statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_tbl_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"library(dplyr) library(survival)  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"OS\") fit <- survfit(   formula = Surv(AVAL, 1 - CNSR) ~ ARMCD,   data = adtte ) h_tbl_median_surv(fit_km = fit) #>        N Median        95% CI #> ARM A 69  974.6   (687, 1625) #> ARM B 73  727.8 (555.8, 1156) #> ARM C 58  632.3   (393, 1001)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"Helper function count number patients fraction patients according highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var, direction interest specified direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"h_worsen_counter(df, id, .var, baseline_var, direction_var)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"df (data.frame) data set containing analysis variables. id (string) subject variable name. .var (string) single variable name passed rtables requested statistics function. baseline_var (string) name baseline lab grade variable. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\".","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/h_worsen_counter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  # `h_worsen_counter` h_worsen_counter(   df %>% filter(PARAMCD == \"CRP\" & GRADDR == \"Low\"),   id = \"USUBJID\",   .var = \"ATOXGR\",   baseline_var = \"BTOXGR\",   direction_var = \"GRADDR\" ) #> $fraction #> $fraction$`1` #>   num denom  #>    25   180  #>  #> $fraction$`2` #>   num denom  #>    15   186  #>  #> $fraction$`3` #>   num denom  #>    18   191  #>  #> $fraction$`4` #>   num denom  #>    17   196  #>  #> $fraction$Any #>   num denom  #>    75   196  #>  #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to calculate x-tick positions — h_xticks","title":"Helper function to calculate x-tick positions — h_xticks","text":"Calculate positions ticks x-axis. However, xticks already exists kept . based function ggplot2 relies , required graphic patient--risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"h_xticks(data, xticks = NULL, max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to calculate x-tick positions — h_xticks","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to calculate x-tick positions — h_xticks","text":"vector positions use x-axis ticks ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/h_xticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"library(dplyr) library(survival)  data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot()  h_xticks(data) #> [1]    0 1000 2000 3000 4000 5000 h_xticks(data, xticks = seq(0, 3000, 500)) #> [1]    0  500 1000 1500 2000 2500 3000 h_xticks(data, xticks = 500) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 h_xticks(data, xticks = 500, max_time = 6000) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 h_xticks(data, xticks = c(0, 500), max_time = 300) #> [1]   0 500 h_xticks(data, xticks = 500, max_time = 300) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"imputation_rule(   df,   x_stats,   stat,   imp_rule,   post = FALSE,   avalcat_var = \"AVALCAT1\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"df (data.frame) data set containing analysis variables. x_stats (named list) named list statistics, typically results s_summary(). stat (string) statistic return value/NA level according imputation rule applied. imp_rule (string) imputation rule setting. Set \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. post (flag) whether data corresponds post-dose time-point (defaults FALSE). parameter used imp_rule set \"1/3\". avalcat_var (string) name variable indicates whether row df corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable avalcat_var must present df.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"list containing statistic value (val) NA level (na_str) displayed according specified imputation rule.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/imputation_rule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"set.seed(1) df <- data.frame(   AVAL = runif(50, 0, 1),   AVALCAT1 = sample(c(1, \"BLQ\"), 50, replace = TRUE) ) x_stats <- s_summary(df$AVAL) imputation_rule(df, x_stats, \"max\", \"1/3\") #> $val #>       max  #> 0.9919061  #>  #> $na_str #> [1] \"ND\" #>  imputation_rule(df, x_stats, \"geom_mean\", \"1/3\") #> $val #> [1] NA #>  #> $na_str #> [1] \"NE\" #>  imputation_rule(df, x_stats, \"mean\", \"1/2\") #> $val #> [1] NA #>  #> $na_str #> [1] \"ND\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence rate estimation — incidence_rate","title":"Incidence rate estimation — incidence_rate","text":"analyze function estimate_incidence_rate() creates layout element estimate event rate adjusted person-years risk, otherwise known incidence rate. primary analysis variable specified via vars person-years risk. addition variable, n_events variable number events observed (value 1 means event observed 0 means event observed) must also specified.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence rate estimation — incidence_rate","text":"","code":"estimate_incidence_rate(   lyt,   vars,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   na_str = default_na_str(),   nested = TRUE,   summarize = FALSE,   label_fmt = \"%s - %.labels\",   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = c(\"person_years\", \"n_events\", \"rate\", \"rate_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_incidence_rate(   df,   .var,   n_events,   is_event = lifecycle::deprecated(),   id_var = \"USUBJID\",   control = control_incidence_rate() )  a_incidence_rate(   df,   labelstr = \"\",   .var,   .df_row,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   .stats = NULL,   .formats = c(person_years = \"xx.x\", n_events = \"xx\", rate = \"xx.xx\", rate_ci =     \"(xx.xx, xx.xx)\", n_unique = \"xx\", n_rate = \"xx (xx.x)\"),   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   label_fmt = \"%s - %.labels\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence rate estimation — incidence_rate","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . n_events (string) name integer variable indicating whether event observed (1) (0). id_var (string) name variable used patient identifier \"n_unique\" included .stats. Defaults \"USUBJID\". control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level (proportion) confidence level estimated incidence rate. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric) time unit desired output (person-years). na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. summarize (flag) whether function act analyze function (summarize = FALSE), summarize function (summarize = TRUE). Defaults FALSE. label_fmt (string) labels formatted row split occurs summarize = TRUE. string use \"%s\" represent row split levels, \"%.labels\" represent labels supplied .labels argument. Defaults \"%s - %.labels\". ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"estimate_incidence_rate\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_incidence_rate() table layout. s_incidence_rate() returns following statistics: person_years: Total person-years risk. n_events: Total number events observed. rate: Estimated incidence rate. rate_ci: Confidence interval incidence rate. n_unique: Total number patients least one event observed. n_rate: Total number events observed & estimated incidence rate. a_incidence_rate() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_incidence_rate(): Statistics function estimates incidence rate associated confidence interval. a_incidence_rate(): Formatted analysis function used afun estimate_incidence_rate().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence rate estimation — incidence_rate","text":"","code":"df <- data.frame(   USUBJID = as.character(seq(6)),   CNSR = c(0, 1, 1, 0, 0, 0),   AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\")),   STRATA1 = factor(c(\"X\", \"Y\", \"Y\", \"X\", \"X\", \"Y\")) ) df$n_events <- 1 - df$CNSR  basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     control = control_incidence_rate(       input_time_unit = \"month\",       num_pt_year = 100     )   ) %>%   build_table(df) #>                                            A                 B        #>                                          (N=3)             (N=3)      #> ————————————————————————————————————————————————————————————————————— #> Total patient-years at risk               3.8               5.2       #> Number of adverse events observed          1                 3        #> AE rate per 100 patient-years            26.20             57.23      #> 95% CI                              (-25.15, 77.55)   (-7.53, 122.00)  # summarize = TRUE basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"STRATA1\", child_labels = \"visible\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     .stats = c(\"n_unique\", \"n_rate\"),     summarize = TRUE,     label_fmt = \"%.labels\"   ) %>%   build_table(df) #>                                                                          A         B    #>                                                                        (N=3)     (N=3)  #> ——————————————————————————————————————————————————————————————————————————————————————— #> X                                                                                       #>   Total number of patients with at least one adverse event               1         2    #>   Number of adverse events observed (AE rate per 100 patient-years)   1 (9.9)   2 (5.1) #> Y                                                                                       #>   Total number of patients with at least one adverse event               0         1    #>   Number of adverse events observed (AE rate per 100 patient-years)   0 (0.0)   1 (4.3)  a_incidence_rate(   df,   .var = \"AVAL\",   .df_row = df,   n_events = \"n_events\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>       row_name formatted_cell indent_mod #> 1 person_years          108.7          0 #> 2     n_events              4          0 #> 3         rate           3.68          0 #> 4      rate_ci   (0.07, 7.29)          0 #> 5     n_unique              4          0 #> 6       n_rate        4 (3.7)          0 #>                                                           row_label #> 1                                       Total patient-years at risk #> 2                                 Number of adverse events observed #> 3                                     AE rate per 100 patient-years #> 4                                                            95% CI #> 5          Total number of patients with at least one adverse event #> 6 Number of adverse events observed (AE rate per 100 patient-years)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels or names of list elements — labels_or_names","title":"Labels or names of list elements — labels_or_names","text":"Internal helper function working nested statistic function results typically labels names can use.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels or names of list elements — labels_or_names","text":"","code":"labels_or_names(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels or names of list elements — labels_or_names","text":"x (list) list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_or_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels or names of list elements — labels_or_names","text":"character vector labels names list elements.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Update labels according to control specifications — labels_use_control","title":"Update labels according to control specifications — labels_use_control","text":"Given list statistic labels list control parameters, updates labels relevant control specification. example, control element conf_level set 0.9, default label statistic mean_ci updated \"Mean 90% CI\". labels supplied via labels_custom updated regardless control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update labels according to control specifications — labels_use_control","text":"","code":"labels_use_control(labels_default, control, labels_custom = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update labels according to control specifications — labels_use_control","text":"labels_default (named character) named vector statistic labels modify according control specifications. Labels explicitly defined labels_custom affected. control (named list) list control parameters apply adjust default labels. labels_custom (named character) named vector labels customized user affected control.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update labels according to control specifications — labels_use_control","text":"named character vector labels control specifications applied relevant labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/labels_use_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update labels according to control specifications — labels_use_control","text":"","code":"control <- list(conf_level = 0.80, quantiles = c(0.1, 0.83), test_mean = 0.57) get_labels_from_stats(c(\"mean_ci\", \"quantiles\", \"mean_pval\")) %>%   labels_use_control(control = control) #>                          mean_ci                        quantiles  #>                    \"Mean 80% CI\"                \"10% and 83%-ile\"  #>                        mean_pval  #> \"Mean p-value (H0: mean = 0.57)\""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression multivariate column layout function — logistic_regression_cols","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"Layout-creating function creates multivariate column layout summarizing logistic regression results. function wrapper rtables::split_cols_by_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"","code":"logistic_regression_cols(lyt, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_regression_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"layout object suitable passing layouting functions. Adding function rtable layout split table columns corresponding statistics df, estimate, std_error, odds_ratio, ci, pvalue.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression summary table — logistic_summary_by_flag","title":"Logistic regression summary table — logistic_summary_by_flag","text":"Constructor content functions used summarize_logistic() summarize logistic regression results. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression summary table — logistic_summary_by_flag","text":"","code":"logistic_summary_by_flag(   flag_var,   na_str = default_na_str(),   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression summary table — logistic_summary_by_flag","text":"flag_var (string) variable name identifying row used content function. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/logistic_summary_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression summary table — logistic_summary_by_flag","text":"content function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Make names without dots — make_names","title":"Make names without dots — make_names","text":"Make names without dots","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make names without dots — make_names","text":"","code":"make_names(nams)"},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make names without dots — make_names","text":"nams (character) vector original names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/make_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make names without dots — make_names","text":"character vector proper names, use dots contrast make.names().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of months to days — month2day","title":"Conversion of months to days — month2day","text":"Conversion months days. approximative calculation considers month average 30.4375 days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of months to days — month2day","text":"","code":"month2day(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of months to days — month2day","text":"x (numeric(1)) time months.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of months to days — month2day","text":"numeric vector time days.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/month2day.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of months to days — month2day","text":"","code":"x <- c(13.25, 8.15, 1, 2.834) month2day(x) #> [1] 403.29688 248.06563  30.43750  86.25988"},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"Muffled car::Anova — muffled_car_anova","title":"Muffled car::Anova — muffled_car_anova","text":"Applied survival models, car::Anova() signal strata terms dropped model formula present, function deliberately muffles message.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Muffled car::Anova — muffled_car_anova","text":"","code":"muffled_car_anova(mod, test_statistic)"},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Muffled car::Anova — muffled_car_anova","text":"mod (coxph) Cox regression model fitted survival::coxph(). test_statistic (string) method used estimation p.values; wald (default) likelihood.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/muffled_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Muffled car::Anova — muffled_car_anova","text":"output car::Anova(), convergence message muffled.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available (non-missing entries) in a vector — n_available","title":"Number of available (non-missing entries) in a vector — n_available","text":"Small utility function better readability.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available (non-missing entries) in a vector — n_available","text":"","code":"n_available(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of available (non-missing entries) in a vector — n_available","text":"x (vector) vector count non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/n_available.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available (non-missing entries) in a vector — n_available","text":"Number non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Odds ratio estimation — odds_ratio","title":"Odds ratio estimation — odds_ratio","text":"analyze function estimate_odds_ratio() creates layout element compare bivariate responses two groups estimating odds ratio confidence interval. primary analysis variable specified vars group variable. Additional variables can included analysis via variables argument, accepts arm, arm variable, strata, stratification variable. two arm levels present, can combined two groups using groups_list argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Odds ratio estimation — odds_ratio","text":"","code":"estimate_odds_ratio(   lyt,   vars,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   na_str = default_na_str(),   nested = TRUE,   method = \"exact\",   show_labels = \"hidden\",   table_names = vars,   var_labels = vars,   .stats = \"or_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )  a_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Odds ratio estimation — odds_ratio","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. var_labels (character) variable labels. .stats (character) statistics select table. Run get_stats(\"estimate_odds_ratio\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_odds_ratio() table layout. s_odds_ratio() returns named list statistics or_ci (containing est, lcl, ucl) n_tot. a_odds_ratio() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_odds_ratio(): Statistics function estimates odds ratio treatment control. variables list arm strata variable names must passed stratified analysis required. a_odds_ratio(): Formatted analysis function used afun estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Odds ratio estimation — odds_ratio","text":"function uses logistic regression unstratified analyses, conditional logistic regression stratified analyses. Wald confidence interval calculated specified confidence level. stratified analyses, currently implementation conditional likelihood confidence intervals, therefore likelihood confidence interval available option. vars contains responders non-responders odds ratio estimation possible returned values NA.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Odds ratio estimation — odds_ratio","text":"","code":"set.seed(12) dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50), levels = c(\"A\", \"B\")),   strata = factor(sample(c(\"C\", \"D\"), 100, TRUE)) )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_odds_ratio(vars = \"rsp\")  build_table(l, df = dta) #>                               A            B #> ———————————————————————————————————————————— #> Odds Ratio (95% CI)   0.85 (0.38 - 1.88)      # Unstratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> $or_ci #>       est       lcl       ucl  #> 0.8484848 0.3831831 1.8788053  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   # Stratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta,   variables = list(arm = \"grp\", strata = \"strata\") ) #> $or_ci #>       est       lcl       ucl  #> 0.7689750 0.3424155 1.7269154  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   a_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name     formatted_cell indent_mod           row_label #> 1    or_ci 0.85 (0.38 - 1.88)          1 Odds Ratio (95% CI) #> 2    n_tot                100          0             Total n"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference estimation — prop_diff","title":"Proportion difference estimation — prop_diff","text":"analysis function estimate_proportion_diff() creates layout element estimate difference proportion responders within studied population. primary analysis variable, vars, logical variable indicating whether response occurred record. See method parameter options methods use constructing confidence interval proportion difference. stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference estimation — prop_diff","text":"","code":"estimate_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\",   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )  a_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference estimation — prop_diff","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"estimate_proportion_diff\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion_diff() table layout. s_proportion_diff() returns named list elements diff diff_ci. a_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion_diff(): Statistics function estimating difference terms responder proportion. a_proportion_diff(): Formatted analysis function used afun estimate_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proportion difference estimation — prop_diff","text":"performing unstratified analysis, methods \"cmh\", \"strat_newcombe\", \"strat_newcombecc\" permitted.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference estimation — prop_diff","text":"","code":"## \"Mid\" case: 4/4 respond in group A, 1/2 respond in group B. nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_proportion_diff(     vars = \"rsp\",     conf_level = 0.90,     method = \"ha\"   )  build_table(l, df = dta) #>                                        A         B #> —————————————————————————————————————————————————— #> Difference in Response rate (%)       12.0         #>   90% CI (Anderson-Hauck)         (-5.4, 29.4)      s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> $diff #> [1] 12 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -5.374519 29.374519 #> attr(,\"label\") #> [1] \"90% CI (Anderson-Hauck)\" #>   # CMH example with strata s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"cmh\" ) #> $diff #> [1] 12.05847 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -2.67057 26.78750 #> attr(,\"label\") #> [1] \"90% CI (CMH, without correction)\" #>   a_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                       row_label #> 1     diff           12.0          0 Difference in Response rate (%) #> 2  diff_ci   (-5.4, 29.4)          1         90% CI (Anderson-Hauck)"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Difference test for two proportions — prop_diff_test","title":"Difference test for two proportions — prop_diff_test","text":"analyze function test_proportion_diff() creates layout element test difference two proportions. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use calculate p-value. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Difference test for two proportions — prop_diff_test","text":"","code":"test_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\"),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )  a_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Difference test for two proportions — prop_diff_test","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"test_proportion_diff\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_test_proportion_diff() table layout. s_test_proportion_diff() returns named list single item pval attribute label describing method used. p-value tests null hypothesis proportions two groups . a_test_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_test_proportion_diff(): Statistics function tests difference two proportions. a_test_proportion_diff(): Formatted analysis function used afun test_proportion_diff().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/prop_diff_test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Difference test for two proportions — prop_diff_test","text":"","code":"dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50)),   strata = factor(rep(c(\"V\", \"W\", \"X\", \"Y\", \"Z\"), each = 20)) )  # With `rtables` pipelines. l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   test_proportion_diff(     vars = \"rsp\",     method = \"cmh\", variables = list(strata = \"strata\")   )  build_table(l, df = dta) #>                                              A      B #> ————————————————————————————————————————————————————— #>   p-value (Cochran-Mantel-Haenszel Test)   1.0000"},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table pruning — prune_occurrences","title":"Occurrence table pruning — prune_occurrences","text":"Family constructor condition functions flexibly prune occurrence tables. condition functions always return whether row result higher threshold. Since class CombinationFunction() can logically combined condition functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table pruning — prune_occurrences","text":"","code":"keep_rows(row_condition)  keep_content_rows(content_row_condition)  has_count_in_cols(atleast, ...)  has_count_in_any_col(atleast, ...)  has_fraction_in_cols(atleast, ...)  has_fraction_in_any_col(atleast, ...)  has_fractions_difference(atleast, ...)  has_counts_difference(atleast, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table pruning — prune_occurrences","text":"row_condition (CombinationFunction) condition function works individual analysis rows flags whether kept pruned table. content_row_condition (CombinationFunction) condition function works individual first content rows leaf tables flags whether leaf tables kept pruned table. atleast (numeric(1)) threshold met order keep row. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows() returns pruning function can used rtables::prune_table() prune rtables table. keep_content_rows() returns pruning function checks condition first content row leaf tables table. has_count_in_cols() returns condition function sums counts specified column. has_count_in_any_col() returns condition function compares counts specified columns threshold. has_fraction_in_cols() returns condition function sums counts specified column, computes fraction dividing total column counts. has_fraction_in_any_col() returns condition function looks fractions specified columns checks whether fulfill threshold. has_fractions_difference() returns condition function extracts fractions specified column, computes difference minimum maximum. has_counts_difference() returns condition function extracts counts specified column, computes difference minimum maximum.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows(): Constructor creating pruning functions based row condition function. removes analysis rows (TableRow) pruned, .e., fulfill row condition. removes sub-tree children left. keep_content_rows(): Constructor creating pruning functions based condition (first) content row leaf tables. removes leaf tables first content row fulfill condition. check individual rows. proceeds recursively removing sub tree children left. has_count_in_cols(): Constructor creating condition functions total counts specified columns. has_count_in_any_col(): Constructor creating condition functions counts specified columns satisfying threshold. has_fraction_in_cols(): Constructor creating condition functions total fraction specified columns. has_fraction_in_any_col(): Constructor creating condition functions fraction specified columns. has_fractions_difference(): Constructor creating condition function checks difference fractions reported specified column. has_counts_difference(): Constructor creating condition function checks difference counts reported specified column.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Occurrence table pruning — prune_occurrences","text":"Since table specifications worded positively, name constructor condition functions positively, . However, note result keep_rows() says pruned, conform rtables::prune_table() interface.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/prune_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table pruning — prune_occurrences","text":"","code":"# \\donttest{ tab <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   split_rows_by(\"STRATA1\") %>%   summarize_row_groups() %>%   analyze_vars(\"COUNTRY\", .stats = \"count_fraction\") %>%   build_table(DM) # }  # \\donttest{ # `keep_rows` is_non_empty <- !CombinationFunction(all_zero_or_na) prune_table(tab, keep_rows(is_non_empty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # `keep_content_rows` # \\donttest{ more_than_twenty <- has_count_in_cols(atleast = 20L, col_names = names(tab)) prune_table(tab, keep_content_rows(more_than_twenty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>     CHE                         0            0              0        #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     RUS                         0            0              0        #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     NGA                         0            0              0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>     CHE                         0            0              0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #>     JPN                         0            0              0        #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        # }  # \\donttest{ more_than_one <- has_count_in_cols(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_count_in_any_col` any_more_than_one <- has_count_in_any_col(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(any_more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fraction_in_cols` more_than_five_percent <- has_fraction_in_cols(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #> BLACK OR AFRICAN AMERICAN                                            #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    # }  # \\donttest{ # `has_fraction_in_any_col` any_atleast_five_percent <- has_fraction_in_any_col(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(any_atleast_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fractions_difference` more_than_five_percent_diff <- has_fractions_difference(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ more_than_one_diff <- has_counts_difference(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":null,"dir":"Reference","previous_headings":"","what":"Re-implemented range() default S3 method for numerical objects — range_noinf","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"function returns c(NA, NA) instead c(-Inf, Inf) zero-length data without warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"","code":"range_noinf(x, na.rm = FALSE, finite = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"x (numeric) sequence numbers range computed. na.rm (flag) flag indicating NA omitted. finite (flag) flag indicating non-finite elements removed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/range_noinf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"2-element vector class numeric.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Reapply variable labels — reapply_varlabels","title":"Reapply variable labels — reapply_varlabels","text":"helper function used tests.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reapply variable labels — reapply_varlabels","text":"","code":"reapply_varlabels(x, varlabels, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reapply variable labels — reapply_varlabels","text":"x (vector) vector elements needs new labels. varlabels (character) vector labels x. ... parameters added list.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/reapply_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reapply variable labels — reapply_varlabels","text":"x variable labels reapplied.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"tabulate_rsp_biomarkers() function creates layout element tabulate estimated biomarker effects binary response endpoint across subgroups, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"tabulate_rsp_biomarkers(   df,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\"),   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_rsp_biomarkers(). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"rtables table summarizing biomarker effects binary response subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"contrast tabulate_rsp_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f )  # \\donttest{ ## Table with default columns. tabulate_rsp_biomarkers(df) #>                                  Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                               #>   All Patients                     200        164          82.0%          1.00      (0.95, 1.05)       0.8530     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          0.93      (0.85, 1.01)       0.0845     #>     MEDIUM                         68          58          85.3%          0.99      (0.88, 1.11)       0.8190     #>     HIGH                           62          53          85.5%          1.06      (0.96, 1.18)       0.2419     #> Continuous Level Biomarker 1                                                                                      #>   All Patients                     200        164          82.0%          0.98      (0.88, 1.08)       0.6353     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          1.15      (0.95, 1.40)       0.1584     #>     MEDIUM                         68          58          85.3%          0.88      (0.73, 1.06)       0.1700     #>     HIGH                           62          53          85.5%          0.88      (0.72, 1.08)       0.2104      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_rsp_biomarkers(   df = df,   vars = c(\"n_rsp\", \"ci\", \"n_tot\", \"prop\", \"or\") )  ## Finally produce the forest plot. g_forest(tab, xlim = c(0.7, 1.4))  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate binary response by subgroup — response_subgroups","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups() function creates layout element tabulate binary response subgroup, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"tabulate_rsp_subgroups(   lyt,   df,   vars = c(\"n_tot\", \"n\", \"prop\", \"or\", \"ci\"),   groups_lists = list(),   label_all = \"All Patients\",   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\") )  a_response_subgroups(   .formats = list(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\", riskdiff = \"xx.x (xx.x - xx.x)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate binary response by subgroup — response_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_rsp_subgroups(). vars (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$prop$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate binary response by subgroup — response_subgroups","text":"rtables table summarizing binary response subgroup. a_response_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate binary response by subgroup — response_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups(): Table-creating function creates table summarizing binary response subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_response_subgroups(): Formatted analysis function used afun tabulate_rsp_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # Unstratified analysis. df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) df #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Stratified analysis. df_strat <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\"), strata = \"STRATA1\"),   data = adrs_f ) df_strat #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6343899 1.1537821  6.015009       0.95 All Patients    ALL #> 2        78 9.5946605 2.0379337 45.171985       0.95            F    SEX #> 3        64 0.8947158 0.2936803  2.725809       0.95            M    SEX #> 4        50 3.5976656 1.0101319 12.813374       0.95          LOW BMRKR2 #> 5        49 2.6242168 0.5162572 13.339308       0.95       MEDIUM BMRKR2 #> 6        43 2.2816865 0.4116391 12.647228       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Grouping of the BMRKR2 levels. df_grouped <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $prop #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Table with default columns basic_table() %>%   tabulate_rsp_subgroups(df) #>                                             B: Placebo           A: Drug X                                  #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI     #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                         #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45) #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)  # Table with selected columns basic_table() %>%   tabulate_rsp_subgroups(     df = df,     vars = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\")   ) #>                                                    B: Placebo                       A: Drug X                                         #> Baseline Risk Factors          Total n   n    Responders   Response (%)   n    Responders   Response (%)   Odds Ratio      95% CI     #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73       50          68.5%       69       59          85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                                                   #>   F                              78      40       25          62.5%       38       36          94.7%         10.80      (2.27, 51.45) #>   M                              64      33       25          75.8%       31       23          74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                                          #>   LOW                            50      24       13          54.2%       26       21          80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23       17          73.9%       26       23          88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26       20          76.9%       17       15          88.2%          2.25      (0.40, 12.75)  # Table with risk difference column added basic_table() %>%   tabulate_rsp_subgroups(     df,     riskdiff = control_riskdiff(       arm_x = levels(df$prop$arm)[1],       arm_y = levels(df$prop$arm)[2]     )   ) #>                                             B: Placebo           A: Drug X                                                                 #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI       Risk Difference (%) (95% CI) #> —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)        -17.0 (-30.5 - -3.5)     #> Sex                                                                                                                                        #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45)      -32.2 (-48.8 - -15.6)     #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)         1.6 (-19.7 - 22.8)      #> Continuous Level Biomarker 2                                                                                                               #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57)       -26.6 (-51.6 - -1.6)     #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39)       -14.5 (-36.3 - 7.2)      #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)       -11.3 (-33.6 - 11.0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert rtable objects to ggplot objects — rtable2gg","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"Given rtables::rtable() object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package. table titles /footnotes ignored.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"rtable2gg(tbl, fontsize = 12, colwidths = NULL, lbl_col_padding = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"tbl (VTableTree)rtables table object. fontsize (numeric(1)) font size. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtable2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"dta <- data.frame(   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   AVAL    = c(9:1, rep(NA, 9)) )  lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  tbl <- build_table(lyt, df = dta)  rtable2gg(tbl)   rtable2gg(tbl, fontsize = 15, colwidths = c(2, 1, 1, 1))"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for accessing information from rtables — rtables_access","title":"Helper functions for accessing information from rtables — rtables_access","text":"couple functions help accessing data rtables objects. Currently work occurrence tables, defined count first element fraction second element cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"h_row_first_values(table_row, col_names = NULL, col_indices = NULL)  h_row_counts(table_row, col_names = NULL, col_indices = NULL)  h_row_fractions(table_row, col_names = NULL, col_indices = NULL)  h_col_counts(table, col_names = NULL, col_indices = NULL)  h_content_first_row(table)  is_leaf_table(table)  check_names_indices(table_row, col_names = NULL, col_indices = NULL)"},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for accessing information from rtables — rtables_access","text":"table_row (TableRow) analysis row occurrence table. col_names (character) names columns extract . col_indices (integer) indices columns extract . col_names provided, inferred names table_row. Note currently works well single column split. table (VTableNodeInfo) occurrence table row.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values() returns vector numeric values. h_row_counts() returns vector numeric values. h_row_fractions() returns vector proportions. h_col_counts() returns vector column counts. h_content_first_row() returns row rtables table. is_leaf_table() returns logical value indicating whether current table leaf. check_names_indices returns column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values(): Helper function extract first values content cell specified columns TableRow. Defaults columns. h_row_counts(): Helper function extracts row values checks convertible integers (integerish values). h_row_fractions(): Helper function extract fractions specified columns TableRow. specifically extracts second values content cell checks fraction. h_col_counts(): Helper function extract column counts specified columns table. h_content_first_row(): Helper function get first row content table current table. is_leaf_table(): Helper function says whether current table leaf tree. check_names_indices(): Internal helper function tests standard inputs column indices.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/rtables_access.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   analyze(\"AGE\", function(x) {     list(       \"mean (sd)\" = rcell(c(mean(x), sd(x)), format = \"xx.x (xx.x)\"),       \"n\" = length(x),       \"frac\" = rcell(c(0.1, 0.1), format = \"xx (xx)\")     )   }) %>%   build_table(tern_ex_adsl) %>%   prune_table() tree_row_elem <- collect_leaves(tbl[2, ])[[1]] result <- max(h_row_first_values(tree_row_elem)) result #> [1] 35.31214  # Row counts (integer values) # h_row_counts(tree_row_elem) # Fails because there are no integers # Using values with integers tree_row_elem <- collect_leaves(tbl[3, ])[[1]] result <- h_row_counts(tree_row_elem) # result  # Row fractions tree_row_elem <- collect_leaves(tbl[4, ])[[1]] h_row_fractions(tree_row_elem) #>      A: Drug X     B: Placebo C: Combination  #>            0.1            0.1            0.1"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman analysis — s_bland_altman","title":"Bland-Altman analysis — s_bland_altman","text":"Statistics function uses Bland-Altman method assess agreement two numerical vectors calculates variety statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"s_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman analysis — s_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman analysis — s_bland_altman","text":"named list following elements: df difference_mean ci_mean difference_sd difference_se upper_agreement_limit lower_agreement_limit agreement_limit_se upper_agreement_limit_ci lower_agreement_limit_ci t_value n","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  s_bland_altman(x, y, conf_level = 0.9) #> $df #>    average difference #> 1      3.0         -4 #> 2      7.5         -3 #> 3     12.0         -2 #> 4     16.5         -1 #> 5     21.0          0 #> 6     25.5          1 #> 7     30.0          2 #> 8     34.5          3 #> 9     39.0          4 #> 10    43.5          5 #> 11    48.0          6 #> 12    52.5          7 #>  #> $difference_mean #> [1] 1.5 #>  #> $ci_mean #> [1] -0.3692162  3.3692162 #>  #> $difference_sd #> [1] 3.605551 #>  #> $difference_se #> [1] 1.040833 #>  #> $upper_agreement_limit #> [1] 7.430604 #>  #> $lower_agreement_limit #> [1] -4.430604 #>  #> $agreement_limit_se #> [1] 1.802776 #>  #> $upper_agreement_limit_ci #> [1]  4.193027 10.668181 #>  #> $lower_agreement_limit_ci #> [1] -7.668181 -1.193027 #>  #> $t_value #> [1] 1.795885 #>  #> $n #> [1] 12 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate Cox model - summarized results — s_cox_multivariate","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"Analyses based multivariate Cox model usually performed Controlled Substance Reporting regulatory documents serve exploratory purposes (e.g., publication). practice, model usually includes main effects (without interaction terms). produces hazard ratio estimates covariates included model. analysis follows principles (e.g., stratified vs. unstratified analysis tie handling) usual Cox model analysis. Since usually pre-specified hypothesis testing analysis, p.values need interpreted caution. (Statistical Analysis Clinical Trials Data R, NEST's bookdown)","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"s_cox_multivariate(   formula,   data,   conf_level = 0.95,   pval_method = c(\"wald\", \"likelihood\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"formula (formula) formula corresponding investigated survival::Surv() survival model including covariates. data (data.frame) data frame includes variable formula covariates. conf_level (proportion) confidence level hazard ratio interval estimations. Default 0.95. pval_method (string) method used estimation p-values, one \"wald\" (default) \"likelihood\". ... optional parameters passed survival::coxph(). Can include ties, character string specifying method tie handling, one exact (default), efron, breslow.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"list elements mod, msum, aov, coef_inter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"output limited single effect terms. Work ongoing estimation interaction terms scope defined  Global Data Standards Repository (GDS_Standard_TLG_Specs_Tables_2.doc).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/s_cox_multivariate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte adtte_f <- subset(adtte, PARAMCD == \"OS\") # _f: filtered adtte_f <- filter(   adtte_f,   PARAMCD == \"OS\" &     SEX %in% c(\"F\", \"M\") &     RACE %in% c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\") ) adtte_f$SEX <- droplevels(adtte_f$SEX) adtte_f$RACE <- droplevels(adtte_f$RACE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert strings to NA — sas_na","title":"Convert strings to NA — sas_na","text":"SAS imports missing data empty strings strings whitespaces . helper function can used convert values NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(x, empty = TRUE, whitespaces = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert strings to NA — sas_na","text":"x (factor character) values missing values substituted. empty (flag) TRUE, empty strings get replaced NA. whitespaces (flag) TRUE, strings made whitespaces get replaced NA.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert strings to NA — sas_na","text":"x \"\" /whitespace-values substituted NA, depending values empty whitespaces.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/sas_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(c(\"1\", \"\", \" \", \"   \", \"b\")) #> [1] \"1\" NA  NA  NA  \"b\" sas_na(factor(c(\"\", \" \", \"b\"))) #> [1] <NA> <NA> b    #> Levels: b  is.na(sas_na(c(\"1\", \"\", \" \", \"   \", \"b\"))) #> [1] FALSE  TRUE  TRUE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table sorting — score_occurrences","title":"Occurrence table sorting — score_occurrences","text":"Functions score occurrence table subtables rows can used sorting occurrence tables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table sorting — score_occurrences","text":"","code":"score_occurrences(table_row)  score_occurrences_cols(...)  score_occurrences_subtable(...)  score_occurrences_cont_cols(...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table sorting — score_occurrences","text":"table_row (TableRow) analysis row occurrence table. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences() returns sum counts across columns table row. score_occurrences_cols() returns function sums counts across specified columns table row. score_occurrences_subtable() returns function sums counts subtable across specified columns. score_occurrences_cont_cols() returns function sums counts first content row specified columns.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences(): Scoring function sums counts across columns. fail anything else counts used. score_occurrences_cols(): Scoring functions can produced constructor include specific columns scoring. See h_row_counts() information. score_occurrences_subtable(): Scoring functions produced constructor can used subtables: sum specified column counts subtable. useful available content row summing counts. score_occurrences_cont_cols(): Produces score function sorting table summing first content row specified columns. Note extending rtables::cont_n_onecol() rtables::cont_n_allcols().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/score_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table sorting — score_occurrences","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(     vars = \"USUBJID\",     .stats = c(\"unique\"),     .labels = c(\"Total number of patients with at least one event\")   ) %>%   split_rows_by(\"AEBODSYS\", child_labels = \"visible\", nested = FALSE) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       \"Total number of patients with at least one event\",       \"Total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\")  tbl <- build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) %>%   prune_table()  tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_occurrences)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_cols_a_and_b <- score_occurrences_cols(col_names = c(\"A: Drug X\", \"B: Placebo\"))  # Note that this here just sorts the AEDECOD inside the AEBODSYS. The AEBODSYS are not sorted. # That would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_cols_a_and_b)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_subtable_all <- score_occurrences_subtable(col_names = names(tbl))  # Note that this code just sorts the AEBODSYS, not the AEDECOD within AEBODSYS. That # would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\"), scorefun = score_subtable_all, decreasing = FALSE)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"split_cols_by_groups(lyt, var, groups_list = NULL, ref_group = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split columns by groups of levels — split_cols_by_groups","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. ref_group (data.frame vector) data corresponding reference group. ... additional arguments rtables::split_cols_by() order. instance, control formats (format), add joint column groups (incl_all).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split columns by groups of levels — split_cols_by_groups","text":"layout object suitable passing layouting functions. Adding function rtable layout add column split including given groups table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/split_cols_by_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"# 1 - Basic use  # Without group combination `split_cols_by_groups` is # equivalent to [rtables::split_cols_by()]. basic_table() %>%   split_cols_by_groups(\"ARM\") %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X   B: Placebo   C: Combination #>         (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————— #> Mean     34.91       33.02          34.57       # Add a reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X   B: Placebo   C: Combination #>              (N=121)     (N=106)        (N=129)     #> ——————————————————————————————————————————————————— #> Diff Mean     1.89                        1.55       # 2 - Adding group specification  # Manual preparation of the groups. groups <- list(   \"Arms A+B\" = c(\"A: Drug X\", \"B: Placebo\"),   \"Arms A+C\" = c(\"A: Drug X\", \"C: Combination\") )  # Use of split_cols_by_groups without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        Arms A+B   Arms A+C #>        (N=227)    (N=250)  #> —————————————————————————— #> Mean    34.03      34.73    # Including differentiated output in the reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups, ref_group = \"Arms A+B\") %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff. of Averages\" = rcell(NULL))       } else {         in_rows(\"Diff. of Averages\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>                     Arms A+B   Arms A+C #> ——————————————————————————————————————— #> Diff. of Averages                0.71    # 3 - Binary list dividing factor levels into reference and treatment  # `combine_groups` defines reference and treatment. groups <- combine_groups(   fct = DM$ARM,   ref = c(\"A: Drug X\", \"B: Placebo\") ) groups #> $`A: Drug X/B: Placebo` #> [1] \"A: Drug X\"  \"B: Placebo\" #>  #> $`C: Combination` #> [1] \"C: Combination\" #>   # Use group definition without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X/B: Placebo   C: Combination #>              (N=227)             (N=129)     #> ———————————————————————————————————————————— #> Mean          34.03               34.57       # Use group definition with reference column (first item of groups). basic_table() %>%   split_cols_by_groups(\"ARM\", groups, ref_group = names(groups)[1]) %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> Diff Mean                               0.54"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Split text according to available text width — split_text_grob","title":"Split text according to available text width — split_text_grob","text":"Dynamically wrap text.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split text according to available text width — split_text_grob","text":"","code":"split_text_grob(   text,   x = grid::unit(0.5, \"npc\"),   y = grid::unit(0.5, \"npc\"),   width = grid::unit(1, \"npc\"),   just = \"centre\",   hjust = NULL,   vjust = NULL,   default.units = \"npc\",   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split text according to available text width — split_text_grob","text":"text (string) text wrap. x numeric vector unit object specifying x-values. y numeric vector unit object specifying y-values. width (grid::unit) unit object specifying maximum width text. just justification text     relative (x, y) location.  two values, first     value specifies horizontal justification second value specifies     vertical justification.  Possible string values : \"left\",     \"right\", \"centre\", \"center\", \"bottom\",     \"top\".  numeric values, 0 means left (bottom) alignment     1 means right (top) alignment. hjust numeric vector specifying horizontal justification.     specified, overrides just setting. vjust numeric vector specifying vertical justification.     specified, overrides just setting. default.units string indicating default units use     x y     given numeric vectors. name character identifier. gp object class \"gpar\", typically output     call function gpar.  basically     list graphical parameter settings. vp Grid viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split text according to available text width — split_text_grob","text":"text grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/split_text_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split text according to available text width — split_text_grob","text":"code taken R Graphics Paul Murell, 2nd edition","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Stack multiple grobs — stack_grobs","title":"Stack multiple grobs — stack_grobs","text":"Stack grobs new grob 1 column multiple rows layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stack multiple grobs — stack_grobs","text":"","code":"stack_grobs(   ...,   grobs = list(...),   padding = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stack multiple grobs — stack_grobs","text":"... grobs. grobs (list grob) list grobs. padding (grid::unit) unit length 1, space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stack multiple grobs — stack_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stack_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stack multiple grobs — stack_grobs","text":"","code":"library(grid)  g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid.newpage() grid.draw(stack_grobs(g1, g2, g3))  showViewport()   grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vp1 <- viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(stack_grobs(g1, g2, g3, vp = vp1, name = \"test\"))  showViewport()  grid.ls(grobs = TRUE, viewports = TRUE, print = FALSE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for mean — stat_mean_ci","title":"Confidence interval for mean — stat_mean_ci","text":"Convenient function calculating mean confidence interval. calculates arithmetic well geometric mean. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(   x,   conf_level = 0.95,   na.rm = TRUE,   n_min = 2,   gg_helper = TRUE,   geom_mean = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for mean — stat_mean_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate confidence interval mean. gg_helper (flag) whether output aligned use ggplots. geom_mean (flag) whether geometric mean calculated.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for mean — stat_mean_ci","text":"named vector values mean_ci_lwr mean_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(sample(10), gg_helper = FALSE) #> mean_ci_lwr mean_ci_upr  #>    3.334149    7.665851   p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point()  p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5),   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5, geom_mean = TRUE),   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":null,"dir":"Reference","previous_headings":"","what":"p-Value of the mean — stat_mean_pval","title":"p-Value of the mean — stat_mean_pval","text":"Convenient function calculating two-sided p-value mean.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(x, na.rm = TRUE, n_min = 2, test_mean = 0)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"p-Value of the mean — stat_mean_pval","text":"x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate p-value mean. test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"p-Value of the mean — stat_mean_pval","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_mean_pval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(sample(10)) #>     p_value  #> 0.000278196   stat_mean_pval(rnorm(10), test_mean = 0.5) #>    p_value  #> 0.04235675"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for median — stat_median_ci","title":"Confidence interval for median — stat_median_ci","text":"Convenient function calculating median confidence interval. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(x, conf_level = 0.95, na.rm = TRUE, gg_helper = TRUE)"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for median — stat_median_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. gg_helper (flag) whether output aligned use ggplots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for median — stat_median_ci","text":"named vector values median_ci_lwr median_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Confidence interval for median — stat_median_ci","text":"function adapted DescTools/versions/0.99.35/source","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_median_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(sample(10), gg_helper = FALSE) #> median_ci_lwr median_ci_upr  #>             2             9  #> attr(,\"conf_level\") #> [1] 0.9785156  p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point() p + ggplot2::stat_summary(   fun.data = stat_median_ci,   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference and confidence interval — stat_propdiff_ci","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"Function calculating proportion (risk) difference confidence interval arm X (reference group) arm Y. Risk difference calculated subtracting cumulative incidence arm Y cumulative incidence arm X.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x,   y,   N_x,   N_y,   list_names = NULL,   conf_level = 0.95,   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"x (list integer) list number occurrences arm X (reference group). y (list integer) list number occurrences arm Y. Must equal length x. N_x (numeric(1)) total number records arm X. N_y (numeric(1)) total number records arm Y. list_names (character) names variable/level corresponding pair proportions x y. Must equal length x y. conf_level (proportion) confidence level interval. pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"List proportion differences CIs corresponding pair number occurrences x y. list element consists 3 statistics: proportion difference, CI lower bound, CI upper bound.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/stat_propdiff_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x = list(0.375), y = list(0.01), N_x = 5, N_y = 5, list_names = \"x\", conf_level = 0.9 ) #> $x #> [1]   7.30000 -12.35184  26.95184 #>   stat_propdiff_ci(   x = list(0.5, 0.75, 1), y = list(0.25, 0.05, 0.5), N_x = 10, N_y = 20, pct = FALSE ) #> [[1]] #> [1]  0.0375000 -0.1060891  0.1810891 #>  #> [[2]] #> [1]  0.07250000 -0.09220915  0.23720915 #>  #> [[3]] #> [1]  0.0750000 -0.1231285  0.2731285 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"function wraps estimation stratified percentiles assume approximation large numbers. necessary case proportions strata unequal.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_normal_quantile(vars, weights, conf_level)"},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"vars (character) variable names primary analysis variable iterated . weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"Stratified quantile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/strata_normal_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_data <- table(data.frame(   \"f1\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )) ns <- colSums(strata_data) ests <- strata_data[\"TRUE\", ] / ns vars <- ests * (1 - ests) / ns weights <- rep(1 / length(ns), length(ns))  strata_normal_quantile(vars, weights, 0.95) #> [1] 1.14181"},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Indicate study arm variable in formula — study_arm","title":"Indicate study arm variable in formula — study_arm","text":"use study_arm indicate study arm variable tern formulas.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Indicate study arm variable in formula — study_arm","text":"","code":"study_arm(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Indicate study arm variable in formula — study_arm","text":"x arm information","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/study_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Indicate study arm variable in formula — study_arm","text":"x","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"analyze function summarize_ancova() creates layout element summarize ANCOVA results. function can used analyze multiple endpoints /multiple timepoints within response variable(s) specified vars. Additional variables analysis, namely arm (grouping) variable covariate variables, can defined via variables argument. See details specify variables. interaction term can implemented model needed. interaction variable interact arm variable specified via interaction_term parameter, specific value interaction_term extract ANCOVA results via interaction_y parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"summarize_ancova(   lyt,   vars,   variables,   conf_level,   interaction_y = FALSE,   interaction_item = NULL,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )  a_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". conf_level (proportion) confidence level interval. interaction_y (string flag) selected item inside interaction_item variable used select specific ANCOVA results. interaction needed, default option FALSE. interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"summarize_ancova\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_ancova() table layout. s_ancova() returns named list 5 statistics: n: Count complete sample size group. lsmean: Estimated marginal means group. lsmean_diff: Difference estimated marginal means comparison reference group. working reference group, empty. lsmean_diff_ci: Confidence level difference estimated marginal means comparison reference group. pval: p-value (adjusted multiple comparisons). a_ancova() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_ancova(): Statistics function produces named list results investigated linear model. a_ancova(): Formatted analysis function used afun summarize_ancova().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"basic_table() %>%   split_cols_by(\"Species\", ref_group = \"setosa\") %>%   add_colcounts() %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = NULL),     table_names = \"unadj\",     conf_level = 0.95, var_labels = \"Unadjusted comparison\",     .labels = c(lsmean = \"Mean\", lsmean_diff = \"Difference in Means\")   ) %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = c(\"Sepal.Length\", \"Sepal.Width\")),     table_names = \"adj\",     conf_level = 0.95, var_labels = \"Adjusted comparison (covariates: Sepal.Length and Sepal.Width)\"   ) %>%   build_table(iris) #>                                                                  setosa    versicolor     virginica   #>                                                                  (N=50)      (N=50)         (N=50)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————— #> Unadjusted comparison                                                                                 #>   n                                                                50          50             50      #>   Mean                                                            1.46        4.26           5.55     #>   Difference in Means                                                         2.80           4.09     #>     95% CI                                                                (2.63, 2.97)   (3.92, 4.26) #>     p-value                                                                 <0.0001        <0.0001    #> Adjusted comparison (covariates: Sepal.Length and Sepal.Width)                                        #>   n                                                                50          50             50      #>   Adjusted Mean                                                   2.02        4.19           5.07     #>   Difference in Adjusted Means                                                2.17           3.05     #>     95% CI                                                                (1.96, 2.38)   (2.81, 3.29) #>     p-value                                                                 <0.0001        <0.0001"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize change from baseline values or absolute baseline values — summarize_change","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"analyze function summarize_change() creates layout element summarize change baseline absolute baseline values. primary analysis variable vars indicates numerical change baseline results. Required secondary analysis variables value baseline_flag can supplied function via variables argument. value element name analysis value variable, baseline_flag element name flag variable indicates whether records contain baseline values. Depending baseline flag given, either absolute baseline values (baseline) change baseline values (post-baseline) summarized.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"summarize_change(   lyt,   vars,   variables,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_change_from_baseline(df, .var, variables, na.rm = TRUE, ...)  a_change_from_baseline(df, .var, variables, na.rm = TRUE, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"analyze_vars_numeric) see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. na.rm (flag) whether NA values removed x prior analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_change_from_baseline() table layout. s_change_from_baseline() returns values returned s_summary.numeric(). a_change_from_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_change_from_baseline(): Statistics function summarizes baseline post-baseline visits. a_change_from_baseline(): Formatted analysis function used afun summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"used split visits layout, data subset contains either baseline post-baseline data. data df must either baseline post-baseline visits. Otherwise error thrown.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"library(dplyr)  ## Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup()  results <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test)  results #>                     A                 B               C     #> ——————————————————————————————————————————————————————————— #> V1                                                          #>   n                 2                 1               0     #>   Mean (SD)    7.50 (2.12)    3.00 (<Missing>)    <Missing> #>   Median          7.50              3.00          <Missing> #>   Min - Max    6.00 - 9.00       3.00 - 3.00      <Missing> #> V2                                                          #>   n                 2                 1               0     #>   Mean (SD)   -1.00 (0.00)    -1.00 (<Missing>)   <Missing> #>   Median          -1.00             -1.00         <Missing> #>   Min - Max   -1.00 - -1.00     -1.00 - -1.00     <Missing> #> V3                                                          #>   n                 2                 1               0     #>   Mean (SD)   -2.00 (0.00)    -2.00 (<Missing>)   <Missing> #>   Median          -2.00             -2.00         <Missing> #>   Min - Max   -2.00 - -2.00     -2.00 - -2.00     <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize variables in columns — summarize_colvars","title":"Summarize variables in columns — summarize_colvars","text":"analyze function summarize_colvars() uses statistics function s_summary() analyze variables arranged columns. variables analyze specified table layout via column splits (see rtables::split_cols_by() rtables::split_cols_by_multivar()) prior using summarize_colvars(). function minimal wrapper rtables::analyze_colvars(), function typically used apply different analysis methods rows column variable. use analysis methods column labels, please refer analyze_vars_in_cols() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize variables in columns — summarize_colvars","text":"","code":"summarize_colvars(   lyt,   ...,   na_str = default_na_str(),   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize variables in columns — summarize_colvars","text":"lyt (PreDataTableLayouts) layout analyses added . ... arguments passed s_summary(). na_str (string) string used replace NA empty values output. .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named vector integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize variables in columns — summarize_colvars","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_colvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize variables in columns — summarize_colvars","text":"","code":"dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)),   CHG = c(1:9, rep(NA, 9)) )  ## Default output within a `rtables` pipeline. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars() %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>  ## Selection of statistics, formats and labels also work. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(     .stats = c(\"n\", \"mean_sd\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\")   ) %>%   build_table(dta_test) #>                       A                           B                            C           #>                AVAL       CHG           AVAL             CHG           AVAL         CHG    #> —————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   7.5, 2.1   2.5, 2.1   3.0, <Missing>   7.0, <Missing>   <Missing>   <Missing> #> V2                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   6.5, 2.1   3.5, 2.1   2.0, <Missing>   8.0, <Missing>   <Missing>   <Missing> #> V3                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   5.5, 2.1   4.5, 2.1   1.0, <Missing>   9.0, <Missing>   <Missing>   <Missing>  ## Use arguments interpreted by `s_summary`. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(na.rm = FALSE) %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize functions — summarize_functions","title":"Summarize functions — summarize_functions","text":"functions wrappers rtables::summarize_row_groups(), applying corresponding tern content functions add summary rows given table layout:","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize functions — summarize_functions","text":"add_rowcounts() estimate_multinomial_response() (rtables::analyze()) h_tab_one_biomarker() (probably deprecate) logistic_summary_by_flag() summarize_num_patients() summarize_occurrences() summarize_occurrences_by_grade() summarize_patients_events_in_cols() summarize_patients_exposure_in_cols() Additionally, summarize_coxreg() function utilizes rtables::summarize_row_groups() (combination several rtables functions like rtables::analyze_colvars()) output Cox regression summary table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize Poisson negative binomial regression — summarize_glm_count","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"Summarize results Poisson negative binomial regression. can used analyze count /frequency data using linear model. specifically useful analyzing count data (using Poisson Negative Binomial distribution) result generalized linear model one (e.g. arm) covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"summarize_glm_count(   lyt,   vars,   variables,   distribution,   conf_level,   rate_mean_method = c(\"emmeans\", \"ppmeans\")[1],   weights = stats::weights,   scale = 1,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = get_stats(\"summarize_glm_count\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(n = 0L, rate = 0L, rate_ci = 1L, rate_ratio = 0L, rate_ratio_ci = 1L,     pval = 1L) )  s_glm_count(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   distribution,   conf_level,   rate_mean_method,   weights,   scale = 1 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). conf_level (proportion) confidence level interval. rate_mean_method (character(1)) method used estimate mean odds ratio. Defaults emmeans. see details information. weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans(). scale (numeric(1)) linear scaling factor rate confidence intervals. Defaults 1. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"summarize_glm_count\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_glm_count() table layout. s_glm_count() returns named list 5 statistics: n: Count complete sample size group. rate: Estimated event rate per follow-time. rate_ci: Confidence level estimated rate per follow-time. rate_ratio: Ratio event rates treatment arm reference arm. rate_ratio_ci: Confidence level rate ratio. pval: p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() uses s_glm_count() calculate statistics table. analysis function uses h_glm_count() estimate GLM stats::glm() Poisson Quasi-Poisson distributions MASS::glm.nb() Negative Binomial distribution. methods assume logarithmic link function. point, rates confidence intervals estimated model using either emmeans::emmeans() rate_mean_method = \"emmeans\" h_ppmeans() rate_mean_method = \"ppmeans\". reference group specified building table split_cols_by(ref_group), rate ratio p-value calculated. Otherwise, use emmeans::contrast() calculate rate ratio p-value reference group. Values always estimated method = \"trt.vs.ctrl\" ref equal first arm value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_glm_count(): Statistics function produces named list results investigated Poisson model.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_glm_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"library(dplyr)  anl <- tern_ex_adtte %>% filter(PARAMCD == \"TNE\") anl$AVAL_f <- as.factor(anl$AVAL)  lyt <- basic_table() %>%   split_cols_by(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze_vars(     \"AVAL_f\",     var_labels = \"Number of exacerbations per patient\",     .stats = c(\"count_fraction\"),     .formats = c(\"count_fraction\" = \"xx (xx.xx%)\"),     .labels = c(\"Number of exacerbations per patient\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = NULL),     conf_level = 0.95,     distribution = \"poisson\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (P) exacerbation rate (per year)\",     table_names = \"adjP\",     .stats = c(\"rate\"),     .labels = c(rate = \"Rate\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"quasipoisson\",     rate_mean_method = \"ppmeans\",     var_labels = \"Adjusted (QP) exacerbation rate (per year)\",     table_names = \"adjQP\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   )  build_table(lyt = lyt, df = anl) #>                                                 A: Drug X          B: Placebo       C: Combination  #>                                                   (N=69)             (N=73)             (N=58)      #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Number of exacerbations per patient                                                                 #>   0                                             3 (4.35%)          8 (10.96%)         6 (10.34%)    #>   1                                            11 (15.94%)         9 (12.33%)         6 (10.34%)    #>   2                                            18 (26.09%)        15 (20.55%)         9 (15.52%)    #>   3                                            14 (20.29%)        11 (15.07%)        15 (25.86%)    #>   4                                            10 (14.49%)         9 (12.33%)         9 (15.52%)    #>   5                                             7 (10.14%)         9 (12.33%)         8 (13.79%)    #>   6                                             4 (5.80%)          4 (5.48%)          4 (6.90%)     #>   7                                             2 (2.90%)          8 (10.96%)         0 (0.00%)     #>   10                                            0 (0.00%)          0 (0.00%)          1 (1.72%)     #> Adjusted (P) exacerbation rate (per year)                                                           #>   Rate                                            8.2061             9.1554             7.8551      #> Adjusted (QP) exacerbation rate (per year)                                                          #>   Rate                                            3.1214             3.4860             2.6152      #>     Rate CI                                  (1.7307, 5.6294)   (1.9833, 6.1272)   (1.3661, 5.0065) #>   Rate Ratio                                      0.8954                                0.7502      #>     Rate Ratio CI                            (0.3975, 2.0170)                      (0.3067, 1.8348) #>     p value                                       0.7897                                0.5288"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate logistic regression table — summarize_logistic","title":"Multivariate logistic regression table — summarize_logistic","text":"Layout-creating function summarizes logistic variable regression binary outcome categorical/continuous covariates model statement. covariate category (categorical) specified values (continuous), present degrees freedom, regression parameter estimate standard error (SE) relative reference group category. Report odds ratios covariate category specified values corresponding Wald confidence intervals default allow user specify confidence levels. Report p-value Wald chi-square test null hypothesis covariate effect response model containing specified covariates. Allow option include one two-way interaction present similar output interaction degree freedom.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"summarize_logistic(   lyt,   conf_level,   drop_and_remove_str = \"\",   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate logistic regression table — summarize_logistic","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval. drop_and_remove_str (string) string dropped removed. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate logistic regression table — summarize_logistic","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add logistic regression variable summary table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Multivariate logistic regression table — summarize_logistic","text":"formula, variable names need standard data.frame column names without special characters.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)  # flagging empty strings with \"_\" df <- df_explicit_na(df, na_level = \"_\") df2 <- df_explicit_na(df2, na_level = \"_\")  result1 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df) result1 #>                                       Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Planned Arm Code                              2                                                                                 0.3004  #>   Reference ARM A, n = 64                                                                                                               #>   ARM B, n = 68                               1                  -1.775             1.144           0.17       (<0.01, 3.23)    0.1209  #>   ARM C, n = 52                               1                  17.192            3626.588       >999.99     (0.00, >999.99)   0.9962  #> Age                                                                                                                                     #>   Age                                         1                  0.170              0.095           1.19       (0.93, 1.51)     0.0746  #> Race                                          2                                                                                 0.7967  #>   Reference ASIAN, n = 110                                                                                                              #>   BLACK OR AFRICAN AMERICAN, n = 40           1                  17.923            4001.705       >999.99     (0.00, >999.99)   0.9964  #>   WHITE, n = 34                               1                  -0.656             0.974           0.52       (0.04, 6.37)     0.5002   result2 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df2) result2 #>                                         Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Race                                            2                                                                                 0.9361  #>   Reference ASIAN, n = 110                                                                                                                #>   BLACK OR AFRICAN AMERICAN, n = 40             1                  18.150            3944.701       >999.99     (0.00, >999.99)   0.9963  #>   WHITE, n = 34                                 1                  -0.373             1.026           0.69       (0.05, 9.68)     0.7164  #> Planned Arm Code                                2                                                                                 0.2539  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                 -11.527             6.962                                       0.0978  #>     Age                                                                                                                                   #>       35                                                                                              0.48       (0.01, 15.48)            #>   ARM C, n = 52                                 1                  16.333           20278.387                                     0.9994  #>     Age                                                                                                                                   #>       35                                                                                            >999.99     (0.00, >999.99)           #> Age                                                                                                                                       #>   Age                                           1                  -0.039             0.151                                       0.7981  #>     Planned Arm Code                                                                                                                      #>       ARM A                                                                                           0.96       (0.65, 1.42)             #>       ARM B                                                                                           1.31       (0.92, 1.86)             #>       ARM C                                                                                           0.99      (0.00, >999.99)           #> Interaction of Planned Arm Code * Age           2                                                                                 0.3276  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                  0.308              0.206                                       0.1352  #>   ARM C, n = 52                                 1                  0.029             548.592                                      1.0000"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients — summarize_num_patients","title":"Count number of patients — summarize_num_patients","text":"analyze function analyze_num_patients() creates layout element count total numbers unique non-unique patients. primary analysis variable vars used uniquely identify patients. count_by variable can used identify non-unique patients number patients unique combination values vars count_by returned instead nonunique statistic. required variable can used specify variable required non-missing record included counts. summarize function summarize_num_patients() performs function analyze_num_patients() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients — summarize_num_patients","text":"","code":"analyze_num_patients(   lyt,   vars,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   nested = TRUE,   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   show_labels = c(\"default\", \"visible\", \"hidden\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  summarize_num_patients(   lyt,   var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  s_num_patients(   x,   labelstr,   .N_col,   count_by = NULL,   unique_count_suffix = TRUE )  s_num_patients_content(   df,   labelstr = \"\",   .N_col,   .var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients — summarize_num_patients","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . required (character NULL) name variable required non-missing. count_by (character NULL) name variable combined vars counting nonunique records. unique_count_suffix (flag) whether \"(n)\" suffix added unique_count labels. Defaults TRUE. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .stats (character) statistics select table. Run get_stats(\"summarize_num_patients\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. ... additional arguments lower level functions. x (character factor) vector patient IDs. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. summarize_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. s_num_patients() returns named list 3 statistics: unique: Vector counts percentages. nonunique: Vector counts. unique_count: Counts. s_num_patients_content() returns values s_num_patients().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count number of patients — summarize_num_patients","text":"general, functions starts analyze* expected work like rtables::analyze(), functions starts summarize* based upon rtables::summarize_row_groups(). latter provides value dividing split row column space, , bound fundamental splits, repeated design every page pagination involved.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_num_patients(): Statistics function counts number unique patients, corresponding percentage taken respect total number patients, number non-unique patients. s_num_patients_content(): Statistics function counts number unique patients column (variable), corresponding percentage taken respect total number patients, number non-unique patients column.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients — summarize_num_patients","text":"opposed summarize_num_patients(), function repeat produced rows.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_num_patients.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients — summarize_num_patients","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA, 6, 6, 8, 9)),   ARM = c(\"A\", \"A\", \"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"B\"),   AGE = c(10, 15, 10, 17, 8, 11, 11, 19, 17),   SEX = c(\"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"F\", \"M\") )  # analyze_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(\"USUBJID\", .stats = c(\"unique\")) %>%   build_table(df)  tbl #>                                                  A           B     #>                                                (N=5)       (N=4)   #> —————————————————————————————————————————————————————————————————— #> Number of patients with at least one event   3 (60.0%)   3 (75.0%)  # summarize_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   summarize_num_patients(\"USUBJID\", .stats = \"unique_count\") %>%   build_table(df)  tbl #>         A   B #> ————————————— #> M (n)   2   2 #> F (n)   1   2  # Use the statistics function to count number of unique and nonunique patients. s_num_patients(x = as.character(c(1, 1, 1, 2, 4, NA)), labelstr = \"\", .N_col = 6L) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 5 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>  s_num_patients(   x = as.character(c(1, 1, 1, 2, 4, NA)),   labelstr = \"\",   .N_col = 6L,   count_by = c(1, 1, 2, 1, 1, 1) ) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   # Count number of unique and non-unique patients.  df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = as.character(c(10, 15, 10, 17, 8)) ) s_num_patients_content(df, .N_col = 5, .var = \"USUBJID\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   df_by_event <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = c(10, 15, 10, 17, 8) ) s_num_patients_content(df_by_event, .N_col = 5, .var = \"USUBJID\", count_by = \"EVENT\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 3 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze function analyze_patients_exposure_in_cols() creates layout element count total numbers patients sum analysis value (.e. exposure) across patients columns. primary analysis variable ex_var exposure variable used calculate sum_exposure statistic. id variable used uniquely identify patients data unique patients counted n_patients statistic, var variable used create row split needed. percentage returned part n_patients statistic proportion records correspond unique patient. summarize function summarize_patients_exposure_in_cols() performs function analyze_patients_exposure_in_cols() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred. column split yet performed table, col_split must set TRUE first call analyze_patients_exposure_in_cols() summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"analyze_patients_exposure_in_cols(   lyt,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = 0L,   ... )  summarize_patients_exposure_in_cols(   lyt,   var,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   ...,   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = NULL )  s_count_patients_sum_exposure(   df,   ex_var = \"AVAL\",   id = \"USUBJID\",   labelstr = \"\",   .stats = c(\"n_patients\", \"sum_exposure\"),   .N_col,   custom_label = NULL )  a_count_patients_sum_exposure(   df,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   labelstr = \"\",   .N_col,   .stats,   .formats = list(n_patients = \"xx (xx.x%)\", sum_exposure = \"xx\") )"},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. ex_var (string) name variable df containing exposure values. id (string) subject variable name. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. custom_label (string NULL) provided labelstr empty, used label. col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. na_str (string) string used replace NA empty values output. .stats (character) statistics select table. Run get_stats(\"analyze_patients_exposure_in_cols\") see available statistics function. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted data rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. summarize_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. s_count_patients_sum_exposure() returns named list statistics: n_patients: Number unique patients df. sum_exposure: Sum ex_var across patients df. a_count_patients_sum_exposure() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::analyze_colvars(). summarize_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::summarize_row_groups(). s_count_patients_sum_exposure(): Statistics function counts numbers patients sum exposure across patients. a_count_patients_sum_exposure(): Analysis function used afun rtables::analyze_colvars() within analyze_patients_exposure_in_cols() cfun rtables::summarize_row_groups() within summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"opposed summarize_patients_exposure_in_cols() generates content rows, analyze_patients_exposure_in_cols() generates data rows repeated multiple pages pagination used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/summarize_patients_exposure_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"set.seed(1) df <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 6), rep(\"ARM B\", 6)),   SEX = c(rep(\"Female\", 6), rep(\"Male\", 6)),   AVAL = as.numeric(sample(seq(1, 20), 12)),   stringsAsFactors = TRUE ) adsl <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 2), rep(\"ARM B\", 2)),   SEX = c(rep(\"Female\", 2), rep(\"Male\", 2)),   stringsAsFactors = TRUE )  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE) result <- build_table(lyt, df = df, alt_counts_df = adsl) result #>                                               ARM A                      ARM B                       Total           #>                                       Patients    Person time    Patients    Person time    Patients     Person time #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total patients numbers/person time   6 (100.0%)       46        6 (100.0%)       68        12 (100.0%)       114     #>   Female                             6 (100.0%)       46         0 (0.0%)         0         6 (50.0%)        46      #>   Male                                0 (0.0%)         0        6 (100.0%)       68         6 (50.0%)        68       lyt2 <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(     var = \"AVAL\", col_split = TRUE,     .stats = \"n_patients\", custom_label = \"some custom label\"   ) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE, ex_var = \"AVAL\") result2 <- build_table(lyt2, df = df, alt_counts_df = adsl) result2 #>                       ARM A        ARM B         Total    #>                      Patients     Patients     Patients   #> ————————————————————————————————————————————————————————— #> some custom label   6 (100.0%)   6 (100.0%)   12 (100.0%) #>   Female            6 (100.0%)    0 (0.0%)     6 (50.0%)  #>   Male               0 (0.0%)    6 (100.0%)    6 (50.0%)   lyt3 <- basic_table() %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = TRUE, ex_var = \"AVAL\") result3 <- build_table(lyt3, df = df, alt_counts_df = adsl) result3 #>          Patients    Person time #> ———————————————————————————————— #> Female   6 (50.0%)       46      #> Male     6 (50.0%)       68       # Adding total levels and custom label lyt4 <- basic_table(   show_colcounts = TRUE ) %>%   analyze_patients_exposure_in_cols(     var = \"ARMCD\",     col_split = TRUE,     add_total_level = TRUE,     custom_label = \"TOTAL\"   ) %>%   append_topleft(c(\"\", \"Sex\"))  result4 <- build_table(lyt4, df = df, alt_counts_df = adsl) result4 #>          Patients     Person time #> Sex       (N=12)        (N=12)    #> ————————————————————————————————— #> ARM A    6 (50.0%)        46      #> ARM B    6 (50.0%)        68      #> TOTAL   12 (100.0%)       114      lyt5 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE)  result5 <- build_table(lyt5, df = df, alt_counts_df = adsl) result5 #>                                       Patients     Person time #> —————————————————————————————————————————————————————————————— #> Total patients numbers/person time   12 (100.0%)       114      lyt6 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE, .stats = \"sum_exposure\")  result6 <- build_table(lyt6, df = df, alt_counts_df = adsl) result6 #>                                      Person time #> ———————————————————————————————————————————————— #> Total patients numbers/person time       114      a_count_patients_sum_exposure(   df = df,   var = \"SEX\",   .N_col = nrow(df),   .stats = \"n_patients\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1   Female      6 (50.0%)          0    Female #> 2     Male      6 (50.0%)          0      Male"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers() function creates layout element tabulate estimated effects multiple continuous biomarker variables survival across subgroups, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"tabulate_survival_biomarkers(   df,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   groups_lists = list(),   control = control_coxreg(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_survival_biomarkers(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all please assign label_all parameter within extract_survival_biomarkers() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"rtables table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers(): Table-creating function creates table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"contrast tabulate_survival_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in multiple regression models containing one covariate `RACE`, # as well as one stratification variable `STRATA1`. The subgroups # are defined by the levels of `BMRKR2`.  df <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   label_all = \"Total Patients\",   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1    68           42 858.9952 0.9623210 #> 6       AGE                          Age    68           42 858.9952 1.0360765 #> 7    BMRKR1 Continuous Level Biomarker 1    62           47 727.8043 1.0770946 #> 8       AGE                          Age    62           47 727.8043 1.0009890 #>         lcl      ucl conf_level      pval     pval_label       subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) Total Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) Total Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)            LOW BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)            LOW BMRKR2 #> 5 0.8708694 1.063376       0.95 0.4509368 p-value (Wald)         MEDIUM BMRKR2 #> 6 0.9727439 1.103532       0.95 0.2707796 p-value (Wald)         MEDIUM BMRKR2 #> 7 0.9756250 1.189118       0.95 0.1412524 p-value (Wald)           HIGH BMRKR2 #> 8 0.9678535 1.035259       0.95 0.9541048 p-value (Wald)           HIGH BMRKR2 #>                      var_label row_type #> 1               Total Patients  content #> 2               Total Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually. df_grouped <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1   138           94 777.8929 0.9801709 #> 6       AGE                          Age   138           94 777.8929 1.0236283 #> 7    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 8       AGE                          Age   200          141 753.5176 1.0106406 #>         lcl      ucl conf_level      pval     pval_label        subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald)    All Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald)    All Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)             low BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)             low BMRKR2 #> 5 0.9235465 1.040267       0.95 0.5094582 p-value (Wald)      low/medium BMRKR2 #> 6 0.9859367 1.062761       0.95 0.2224475 p-value (Wald)      low/medium BMRKR2 #> 7 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) low/medium/high BMRKR2 #> 8 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  ## Table with default columns. tabulate_survival_biomarkers(df) #>                                  Total n   Total Events   Median   Hazard Ratio   95% Wald CI    p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                             #>   Total Patients                   200         141        753.5        1.01       (0.99, 1.03)       0.3787     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        1.01       (0.96, 1.06)       0.6736     #>     MEDIUM                         68           42        859.0        1.04       (0.97, 1.10)       0.2708     #>     HIGH                           62           47        727.8        1.00       (0.97, 1.04)       0.9541     #> Continuous Level Biomarker 1                                                                                    #>   Total Patients                   200         141        753.5        1.00       (0.95, 1.05)       0.9646     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        0.99       (0.91, 1.07)       0.8155     #>     MEDIUM                         68           42        859.0        0.96       (0.87, 1.06)       0.4509     #>     HIGH                           62           47        727.8        1.08       (0.98, 1.19)       0.1413      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_survival_biomarkers(   df = df,   vars = c(\"n_tot_events\", \"ci\", \"n_tot\", \"median\", \"hr\"),   time_unit = as.character(adtte_f$AVALU[1]) )  ## Finally produce the forest plot. # \\donttest{ g_forest(tab, xlim = c(0.8, 1.2))  # }"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"analyze function coxph_pairwise() creates layout element analyze pairwise Cox-PH model. function can return statistics including p-value, hazard ratio (HR), HR confidence intervals stratified unstratified Cox-PH models. variable(s) analyzed specified via vars argument stratification factors via strata argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"coxph_pairwise(   lyt,   vars,   strata = NULL,   control = control_coxph(),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"CoxPH\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"pvalue\", \"hr\", \"hr_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )  a_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . strata (character NULL) variable names indicating stratification factors. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"coxph_pairwise\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. strat Please use strata argument instead.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_coxph_pairwise() table layout. s_coxph_pairwise() returns statistics: pvalue: p-value test null hypothesis hazard ratio = 1. hr: Hazard ratio. hr_ci: Confidence interval hazard ratio. n_tot: Total number observations. n_tot_events: Total number events. a_coxph_pairwise() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_coxph_pairwise(): Statistics function analyzes HR, CIs HR, p-value Cox-PH model. a_coxph_pairwise(): Formatted analysis function used afun coxph_pairwise().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  df <- adtte_f %>% filter(ARMCD == \"ARM A\") df_ref_group <- adtte_f %>% filter(ARMCD == \"ARM B\")  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(df = adtte_f) #>                         ARM A       ARM B          ARM C     #>                         (N=69)      (N=73)         (N=58)    #> ———————————————————————————————————————————————————————————— #> Unstratified Analysis                                        #>   p-value (log-rank)                0.0905         0.0086    #>   Hazard Ratio                       1.41           1.81     #>   95% CI                         (0.95, 2.09)   (1.16, 2.84)  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Stratified Analysis\",     strata = \"SEX\",     control = control_coxph(pval_method = \"wald\")   ) %>%   build_table(df = adtte_f) #>                       ARM A       ARM B          ARM C     #>                       (N=69)      (N=73)         (N=58)    #> —————————————————————————————————————————————————————————— #> Stratified Analysis                                        #>   p-value (wald)                  0.0784         0.0066    #>   Hazard Ratio                     1.44           1.89     #>   95% CI                       (0.96, 2.15)   (1.19, 2.98)"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate survival duration by subgroup — survival_duration_subgroups","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups() function creates layout element tabulate survival duration subgroup, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"tabulate_survival_subgroups(   lyt,   df,   vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   groups_lists = list(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot =     \"xx\", hr = list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)),     pval = \"x.xxxx | (<0.0001)\") )  a_survival_subgroups(   .formats = list(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot     = \"xx\", hr = list(format_extreme_values(2L)), ci =     list(format_extreme_values_ci(2L)), pval = \"x.xxxx | (<0.0001)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_survival_subgroups(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all please assign label_all parameter within extract_survival_subgroups() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$survtime$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"rtables table summarizing survival subgroup. a_survival_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups(): Table-creating function creates table summarizing survival subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_survival_subgroups(): Formatted analysis function used afun tabulate_survival_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(   \"ARM\" = adtte_labels[[\"ARM\"]],   \"SEX\" = adtte_labels[[\"SEX\"]],   \"AVALU\" = adtte_labels[[\"AVALU\"]],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- labels  df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   label_all = \"Total Patients\",   data = adtte_f ) df #> $survtime #>           arm  n n_events    median       subgroup    var #> 1  B: Placebo 73       57  727.8043 Total Patients    ALL #> 2   A: Drug X 69       44  974.6402 Total Patients    ALL #> 3  B: Placebo 40       31  599.1772              F    SEX #> 4   A: Drug X 38       24 1016.2982              F    SEX #> 5  B: Placebo 33       26  888.4916              M    SEX #> 6   A: Drug X 31       20  974.6402              M    SEX #> 7  B: Placebo 24       21  735.4722            LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402            LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352         MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197         MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245           HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982           HIGH BMRKR2 #>                       var_label row_type #> 1                Total Patients  content #> 2                Total Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label       subgroup    var                    var_label #> 1 p-value (log-rank) Total Patients    ALL               Total Patients #> 2 p-value (log-rank)              F    SEX                          Sex #> 3 p-value (log-rank)              M    SEX                          Sex #> 4 p-value (log-rank)            LOW BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)         MEDIUM BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank)           HIGH BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   df_grouped <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $survtime #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   ## Table with default columns. basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) #>                                                     B: Placebo               A: Drug X                                      #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI  #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06) #> Sex                                                                                                                         #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96) #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65) #> Continuous Level Biomarker 2                                                                                                #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51) #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61) #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)  ## Table with a manually chosen set of columns: adding \"pval\". basic_table() %>%   tabulate_survival_subgroups(     df = df,     vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\", \"pval\"),     time_unit = adtte_f$AVALU[1]   ) #>                                                     B: Placebo               A: Drug X                                                           #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI    p-value (log-rank) #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06)         0.0905       #> Sex                                                                                                                                              #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96)         0.0341       #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65)         0.7558       #> Continuous Level Biomarker 2                                                                                                                     #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51)         0.4324       #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61)         0.4786       #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)         0.2629"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time analysis — survival_time","title":"Survival time analysis — survival_time","text":"analyze function surv_time() creates layout element analyze survival time calculating survival time median, median confidence interval, quantiles, range (, censored, event patients). primary analysis variable vars time variable secondary analysis variable is_event indicates whether event occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time analysis — survival_time","text":"","code":"surv_time(   lyt,   vars,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"Time to Event\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"median\", \"median_ci\", \"quantiles\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(median_ci = 1L) )  s_surv_time(df, .var, is_event, control = control_surv_time())  a_surv_time(   df,   labelstr = \"\",   .var = NULL,   .df_row = NULL,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time analysis — survival_time","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_time(). possible parameter options : conf_level (proportion) confidence level interval survival time. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" supported. quantiles (numeric) vector length two specify quantiles survival time. ref_fn_censor (flag) whether referential footnotes indicating censored observations printed range statistic included. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Run get_stats(\"surv_time\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time analysis — survival_time","text":"surv_time() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_time() table layout. s_surv_time() returns statistics: median: Median survival time. median_ci: Confidence interval median time. quantiles: Survival time two specified quantiles. range_censor: Survival time range censored observations. range_event: Survival time range observations events. range: Survival time range observations. a_surv_time() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time analysis — survival_time","text":"surv_time(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_time(): Statistics function analyzes survival times. a_surv_time(): Formatted analysis function used afun surv_time().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time analysis — survival_time","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   ) df <- adtte_f %>% filter(ARMCD == \"ARM A\")  basic_table() %>%   split_cols_by(var = \"ARMCD\") %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",     control = control_surv_time(conf_level = 0.9, conf_type = \"log-log\")   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     90% CI               (22.6, 46.5)   (18.3, 29.2)   (12.9, 25.9) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   a_surv_time(   df,   .df_row = df,   .var = \"AVAL\",   is_event = \"is_event\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name formatted_cell indent_mod        row_label #> 1           Median           32.0          0           Median #> 2           95% CI   (22.5, 49.3)          0           95% CI #> 3  25% and 75%-ile     17.4, 65.3          0  25% and 75%-ile #> 4 Range (censored)    0.8 to 63.5          0 Range (censored) #> 5    Range (event)   0.3 to 155.5          0    Range (event) #> 6            Range   0.3 to 155.5          0            Range"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time point analysis — survival_timepoint","title":"Survival time point analysis — survival_timepoint","text":"analyze function surv_timepoint() creates layout element analyze patient survival rates difference survival rates groups given time point. primary analysis variable vars time variable. required inputs time_point, numeric time point interest, is_event, variable indicates whether event occurred. method argument used specify whether want analyze survival estimations (\"surv\"), difference survival control (\"surv_diff\"), (\"\").","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time point analysis — survival_timepoint","text":"","code":"surv_timepoint(   lyt,   vars,   time_point,   is_event,   control = control_surv_timepoint(),   method = c(\"surv\", \"surv_diff\", \"both\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names_suffix = \"\",   var_labels = \"Time\",   show_labels = \"visible\",   .stats = c(\"pt_at_risk\", \"event_free_rate\", \"rate_ci\", \"rate_diff\", \"rate_diff_ci\",     \"ztest_pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = if (method == \"both\") {      c(rate_diff = 1L, rate_diff_ci = 2L,     ztest_pval = 2L)  } else {      c(rate_diff_ci = 1L, ztest_pval = 1L)  } )  s_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  a_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  s_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )  a_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )"},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time point analysis — survival_timepoint","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . time_point (numeric(1)) survival time point interest. is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. method (string)\"surv\" (survival estimations), \"surv_diff\" (difference survival control), \"\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names_suffix (string) optional suffix table_names used rtables avoid warnings duplicate table names. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .stats (character) statistics select table. Run get_stats(\"surv_timepoint\") see available statistics function. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_timepoint() /s_surv_timepoint_diff() table layout depending value method. s_surv_timepoint() returns statistics: pt_at_risk: Patients remaining risk. event_free_rate: Event-free rate (%). rate_se: Standard error event free rate. rate_ci: Confidence interval event free rate. a_surv_timepoint() returns corresponding list formatted rtables::CellValue(). s_surv_timepoint_diff() returns statistics: rate_diff: Event-free rate difference two groups. rate_diff_ci: Confidence interval difference. ztest_pval: p-value test difference 0. a_surv_timepoint_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_timepoint(): Statistics function analyzes survival rate. a_surv_timepoint(): Formatted analysis function used afun surv_timepoint() method = \"surv\". s_surv_timepoint_diff(): Statistics function analyzes difference two survival rates. a_surv_timepoint_diff(): Formatted analysis function used afun surv_timepoint() method = \"surv_diff\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/survival_timepoint.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time point analysis — survival_timepoint","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  # Survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 7   ) %>%   build_table(df = adtte_f) #>                                    ARM A            ARM B            ARM C      #>                                    (N=69)           (N=73)           (N=58)     #> ——————————————————————————————————————————————————————————————————————————————— #> 7 Months                                                                        #>   Patients remaining at risk         54               57               42       #>   Event Free Rate (%)              84.89            79.43            75.50      #>   95% CI                       (76.24, 93.53)   (70.15, 88.71)   (64.33, 86.67)  # Difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"surv_diff\",     .indent_mods = c(\"rate_diff\" = 0L, \"rate_diff_ci\" = 2L, \"ztest_pval\" = 2L)   ) %>%   build_table(df = adtte_f) #>                                   ARM A        ARM B            ARM C      #>                                   (N=69)       (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                   #>   Difference in Event Free Rate                -9.64            -13.03     #>       95% CI                               (-22.80, 3.52)   (-27.59, 1.53) #>       p-value (Z-test)                         0.1511           0.0794      # Survival and difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"both\"   ) %>%   build_table(df = adtte_f) #>                                       ARM A            ARM B            ARM C      #>                                       (N=69)           (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                           #>   Patients remaining at risk            53               53               39       #>   Event Free Rate (%)                 84.89            75.25            71.86      #>   95% CI                          (76.24, 93.53)   (65.32, 85.17)   (60.14, 83.57) #>   Difference in Event Free Rate                        -9.64            -13.03     #>     95% CI                                         (-22.80, 3.52)   (-27.59, 1.53) #>     p-value (Z-test)                                   0.1511           0.0794"},{"path":"https://insightsengineering.github.io/tern/main/reference/tern-package.html","id":null,"dir":"Reference","previous_headings":"","what":"tern Package — tern-package","title":"tern Package — tern-package","text":"Package create tables, listings graphs analyze clinical trials data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tern-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tern Package — tern-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Heng Wang wang.heng@gene.com Francois Collin Adrian Waddell adrian.waddell@gene.com Pawel Rucki pawel.rucki@roche.com Chendi Liao chendi.liao@roche.com Jennifer Li li.jing@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for binomial GLM results — tidy.glm","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"Helper method (broom::tidy()) prepare data frame glm object binomial family.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"# S3 method for class 'glm' tidy(x, conf_level = 0.95, at = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"x (glm) logistic regression model fitted stats::glm() \"binomial\" family. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"data.frame containing tidied model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.glm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for STEP results — tidy.step","title":"Custom tidy method for STEP results — tidy.step","text":"Tidy STEP results tibble format ready plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"# S3 method for class 'step' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for STEP results — tidy.step","text":"x (matrix) results fit_survival_step(). ... used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for STEP results — tidy.step","text":"tibble one row per STEP subgroup. estimates CIs HR scale, respectively. Additional attributes carry metadata also used plotting.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy.step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"library(survival) lung$sex <- factor(lung$sex) vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" ) step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) broom::tidy(step_matrix) #> # A tibble: 10 × 12 #>    `Percentile Center` `Percentile Lower` `Percentile Upper` `Interval Center` #>  *               <dbl>              <dbl>              <dbl>             <dbl> #>  1              0.0909             0                   0.341              50   #>  2              0.182              0                   0.432              54   #>  3              0.273              0.0227              0.523              57   #>  4              0.364              0.114               0.614              59.5 #>  5              0.455              0.205               0.705              62   #>  6              0.545              0.295               0.795              64   #>  7              0.636              0.386               0.886              67   #>  8              0.727              0.477               0.977              69   #>  9              0.818              0.568               1                  71   #> 10              0.909              0.659               1                  74   #> # ℹ 8 more variables: `Interval Lower` <dbl>, `Interval Upper` <dbl>, n <dbl>, #> #   events <dbl>, `Hazard Ratio` <dbl>, se <dbl>, ci_lower <dbl>, #> #   ci_upper <dbl>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"# S3 method for class 'summary.coxph' tidy(x, ...)  # S3 method for class 'coxreg.univar' tidy(x, ...)  # S3 method for class 'coxreg.multivar' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"x (list) result Cox regression model fitted fit_coxreg_univar() (univariate models) fit_coxreg_multivar() (multivariate models). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"broom::tidy() returns: summary.coxph objects,  data.frame columns: Pr(>|z|), exp(coef), exp(-coef), lower .95, upper .95, level, n. coxreg.univar objects, data.frame columns: effect, term, term_label, level, n, hr, lcl, ucl, pval, ci. coxreg.multivar objects, data.frame columns: term, pval, term_label, hr, lcl, ucl, level, ci.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"tidy(summary.coxph): Custom tidy method survival::coxph() summary results. Tidy survival::coxph() results data.frame extract model results. tidy(coxreg.univar): Custom tidy method univariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_univar(). tidy(coxreg.multivar): Custom tidy method multivariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_multivar().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/tidy_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"library(survival) library(broom)  set.seed(1, kind = \"Mersenne-Twister\")  dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  formula <- \"survival::Surv(time, status) ~ armcd + covar1\" msum <- summary(coxph(stats::as.formula(formula), data = dta_bladder)) tidy(msum) #>       Pr(>|z|) exp(coef) exp(-coef)  lower .95 upper .95   level   n #> 1 1.287954e-02 0.6110123   1.636628 0.41442417 0.9008549  armcd2 340 #> 2 6.407916e-04 0.4460731   2.241785 0.28061816 0.7090818 covar12 340 #> 3 5.272933e-06 0.3075864   3.251119 0.18517346 0.5109230 covar13 340 #> 4 2.125359e-08 0.1808795   5.528541 0.09943722 0.3290258 covar14 340  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  tidy(mod1) #>            effect   term        term_label level   n        hr       lcl #> ref    Treatment:  armcd  2 vs control (1)     2 340 0.6386426 0.4557586 #> covar1 Covariate: covar1 A Covariate Label     2 340  0.607037 0.4324571 #>              ucl       pval                   ci #> ref    0.8949131 0.02423805 0.4557586, 0.8949131 #> covar1 0.8520935 0.01257339 0.4324571, 0.8520935 tidy(mod2) #>                           effect   term        term_label level   n        hr #> ref                   Treatment:  armcd  2 vs control (1)     2 340 0.6386426 #> covar1.1              Covariate: covar1 A Covariate Label       340           #> covar1.armcd2/covar11 Covariate: covar1                 1     1     0.6284569 #> covar1.armcd2/covar12 Covariate: covar1                 2     2     0.5806499 #> covar1.armcd2/covar13 Covariate: covar1                 3     3     0.5486103 #> covar1.armcd2/covar14 Covariate: covar1                 4     4     0.6910725 #> covar2.1              Covariate: covar2         Sex (F/M)       340           #> covar2.armcd2/covar2F Covariate: covar2                 F     F     0.6678243 #> covar2.armcd2/covar2M Covariate: covar2                 M     M     0.5954021 #>                             lcl       ucl       pval pval_inter #> ref                   0.4557586 0.8949131 0.02423805            #> covar1.1                     NA        NA             0.9883021 #> covar1.armcd2/covar11 0.3450471 1.1446499                       #> covar1.armcd2/covar12 0.2684726 1.2558239                       #> covar1.armcd2/covar13 0.2226814 1.3515868                       #> covar1.armcd2/covar14 0.2308006 2.0692373                       #> covar2.1                     NA        NA             0.7759013 #> covar2.armcd2/covar2F 0.3649842 1.2219413                       #> covar2.armcd2/covar2M 0.3572772 0.9922368                       #>                                         ci #> ref                   0.4557586, 0.8949131 #> covar1.1                                   #> covar1.armcd2/covar11 0.3450471, 1.1446499 #> covar1.armcd2/covar12 0.2684726, 1.2558239 #> covar1.armcd2/covar13 0.2226814, 1.3515868 #> covar1.armcd2/covar14 0.2308006, 2.0692373 #> covar2.1                                   #> covar2.armcd2/covar2F 0.3649842, 1.2219413 #> covar2.armcd2/covar2M 0.3572772, 0.9922368  multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder ) broom::tidy(multivar_model) #>                       term         pval                        term_label #> armcd.1              armcd                            ARM (reference = 1) #> armcd.2                ARM   0.01232761                                 2 #> covar1.1            covar1 7.209956e-09 A Covariate Label (reference = 1) #> covar1.2 A Covariate Label  0.001120332                                 2 #> covar1.3 A Covariate Label 6.293725e-06                                 3 #> covar1.4 A Covariate Label 3.013875e-08                                 4 #> covar2.1            covar2                      Sex (F/M) (reference = F) #> covar2.2         Sex (F/M)    0.1910521                                 M #>                 hr        lcl       ucl level                     ci #> armcd.1                    NA        NA  <NA>                        #> armcd.2  0.6062777 0.40970194 0.8971710     2   0.4097019, 0.8971710 #> covar1.1                   NA        NA  <NA>                        #> covar1.2 0.4564763 0.28481052 0.7316115     2   0.2848105, 0.7316115 #> covar1.3 0.3069612 0.18386073 0.5124813     3   0.1838607, 0.5124813 #> covar1.4 0.1817017 0.09939435 0.3321668     4 0.09939435, 0.33216684 #> covar2.1                   NA        NA  <NA>                        #> covar2.2  1.289373 0.88087820 1.8873019     M   0.8808782, 1.8873019"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Replicate entries of a vector if required — to_n","title":"Replicate entries of a vector if required — to_n","text":"Replicate entries vector required.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replicate entries of a vector if required — to_n","text":"","code":"to_n(x, n)"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replicate entries of a vector if required — to_n","text":"x (numeric) vector numbers want analyze. n (integer(1)) number entries needed.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replicate entries of a vector if required — to_n","text":"x required length already NULL, otherwise scalar replicated version n entries.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Replicate entries of a vector if required — to_n","text":"function fail x length n /scalar.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert table into matrix of strings — to_string_matrix","title":"Convert table into matrix of strings — to_string_matrix","text":"Helper function use mostly within tests. with_spacesparameter allows test content also indentation table structure. print_txt_to_copy instead facilitate testing development returning well formatted text needs copied pasted expected output.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"to_string_matrix(   x,   widths = NULL,   max_width = NULL,   hsep = formatters::default_hsep(),   with_spaces = TRUE,   print_txt_to_copy = FALSE )"},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert table into matrix of strings — to_string_matrix","text":"x (VTableTree)rtables table object. widths (numeric  NULL) Proposed widths columns x. expected length numeric vector can retrieved ncol(x) + 1 column row names must also considered. max_width (integer(1), string NULL) width title footer (including footnotes) materials word-wrapped . NULL, set current print width session (getOption(\"width\")). set \"auto\", width table (plus table inset) used. Parameter ignored tf_wrap = FALSE. hsep (string) character repeat create header/body separator line. NULL, object value used. \" \", empty separator printed. See default_hsep() information. with_spaces (flag) whether tested table keep indentation relevant spaces. print_txt_to_copy (flag) utility way copy input table directly expected variable instead copying manually.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert table into matrix of strings — to_string_matrix","text":"matrix strings. print_txt_to_copy = TRUE well formatted printout table printed console, ready copied expected value.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/to_string_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"tbl <- basic_table() %>%   split_rows_by(\"SEX\") %>%   split_cols_by(\"ARM\") %>%   analyze(\"AGE\") %>%   build_table(tern_ex_adsl)  to_string_matrix(tbl, widths = ceiling(propose_column_widths(tbl) / 2)) #>  [1] \"       A:                    \" \"      Drug    B: Pl   C: Comb\" #>  [3] \"        X     acebo   ination\" \"—————————————————————————————\" #>  [5] \"F                            \" \"  M   33.68   35.98    36.02 \" #>  [7] \"  e                          \" \"  a                          \" #>  [9] \"  n                          \" \"M                            \" #> [11] \"  M   34.70   35.68    36.28 \" \"  e                          \" #> [13] \"  a                          \" \"  n                          \""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"tryCatch around car::Anova — try_car_anova","title":"tryCatch around car::Anova — try_car_anova","text":"Captures warnings executing car::Anova.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"try_car_anova(mod, test.statistic)"},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tryCatch around car::Anova — try_car_anova","text":"mod lm, aov, glm, multinom, polr     mlm, coxph, coxme, lme, mer, merMod, svyglm, svycoxph,     rlm, clm, clmm, suitable model object. test.statistic generalized linear model, whether calculate     \"LR\" (likelihood-ratio), \"Wald\", \"F\" tests; Cox     Cox mixed-effects model, whether calculate \"LR\" (partial-likelihood ratio)     \"Wald\" tests (\"LR\" tests unavailable Cox models using tt argument); default case linear mixed models fit     lmer, whether calculate Wald \"Chisq\" Kenward-Roger     \"F\" tests Satterthwaite degrees freedom (warning: KR F-tests     can time-consuming).     multivariate linear model, multivariate test statistic compute — one     \"Pillai\", \"Wilks\", \"Hotelling-Lawley\", \"Roy\",     \"Pillai\" default. summary method Anova.mlm     objects permits specification one multivariate     test statistic, default report four.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tryCatch around car::Anova — try_car_anova","text":"list item aov result model error_text captured warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/try_car_anova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"# `car::Anova` on cox regression model including strata and expected # a likelihood ratio test triggers a warning as only Wald method is # accepted.  library(survival)  mod <- coxph(   formula = Surv(time = futime, event = fustat) ~ factor(rx) + strata(ecog.ps),   data = ovarian )"},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Ungroup non-numeric statistics — ungroup_stats","title":"Ungroup non-numeric statistics — ungroup_stats","text":"Ungroups grouped non-numeric statistics within input vectors .formats, .labels, .indent_mods.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ungroup non-numeric statistics — ungroup_stats","text":"","code":"ungroup_stats(x, .formats, .labels, .indent_mods)"},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ungroup non-numeric statistics — ungroup_stats","text":"x (named list numeric) list numeric statistics containing statistics ungroup. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/ungroup_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ungroup non-numeric statistics — ungroup_stats","text":"list modified elements x, .formats, .labels, .indent_mods.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Univariate formula special term — univariate","title":"Univariate formula special term — univariate","text":"special term univariate indicate model fitted individually every variable included univariate.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Univariate formula special term — univariate","text":"","code":"univariate(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Univariate formula special term — univariate","text":"x (character) vector variable names separated commas.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Univariate formula special term — univariate","text":"used within model formula, produces univariate models variable provided.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/univariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Univariate formula special term — univariate","text":"provided alongside pairwise specification, model y ~ ARM + univariate(SEX, AGE, RACE) lead study comparison models y ~ ARM y ~ ARM + SEX y ~ ARM + AGE y ~ ARM + RACE","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Blank for missing input — unlist_and_blank_na","title":"Blank for missing input — unlist_and_blank_na","text":"Helper function use tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blank for missing input — unlist_and_blank_na","text":"","code":"unlist_and_blank_na(x)"},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blank for missing input — unlist_and_blank_na","text":"x (vector) input cell.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/unlist_and_blank_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blank for missing input — unlist_and_blank_na","text":"empty character vector entries x missing (NA), otherwise unlisted version x.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"function wraps iteration procedure allows estimate weights proportional strata. assumes minimize weighted squared length confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"update_weights_strat_wilson(   vars,   strata_qnorm,   initial_weights,   n_per_strata,   max_iterations = 50,   conf_level = 0.95,   tol = 0.001 )"},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"vars (numeric) normalized proportions strata. strata_qnorm (numeric(1)) initial estimation identical weights quantiles. initial_weights (numeric) initial weights used calculate strata_qnorm. can optimized future need estimate better initial weights. n_per_strata (numeric) number elements strata. max_iterations (integer(1)) maximum number iterations tried. Convergence always checked. conf_level (proportion) confidence level interval. tol (numeric(1)) tolerance threshold convergence.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"list 3 elements: n_it, weights, diff_v.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/update_weights_strat_wilson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"vs <- c(0.011, 0.013, 0.012, 0.014, 0.017, 0.018) sq <- 0.674 ws <- rep(1 / length(vs), length(vs)) ns <- c(22, 18, 17, 17, 14, 12)  update_weights_strat_wilson(vs, sq, ws, ns, 100, 0.95, 0.001) #> $n_it #> [1] 3 #>  #> $weights #> [1] 0.2067191 0.1757727 0.1896962 0.1636346 0.1357615 0.1284160 #>  #> $diff_v #> [1] 1.458717e-01 1.497223e-03 1.442189e-06 #>"},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom split functions — utils_split_funs","title":"Custom split functions — utils_split_funs","text":"Collection useful functions expanding core list functions provided rtables. See rtables::custom_split_funs rtables::make_split_fun() information make custom split function. functions work rtables::split_rows_by() argument split_fun modify way split happens. split functions, consider consulting rtables::split_funcs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom split functions — utils_split_funs","text":"","code":"ref_group_position(position = \"first\")  level_order(order)"},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom split functions — utils_split_funs","text":"position (string integer) position use reference group facet. Can \"first\", \"last\", specific position. order (character numeric) vector ordering indices split facets.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom split functions — utils_split_funs","text":"ref_group_position() returns utility function puts reference group first, last certain position needs assigned split_fun. level_order() returns utility function changes original levels' order, depending input order split levels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom split functions — utils_split_funs","text":"ref_group_position(): Split function place reference group facet specific position post-processing stage. level_order(): Split function change level order based integer vector character vector represent split variable's factor levels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/reference/utils_split_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom split functions — utils_split_funs","text":"","code":"library(dplyr)  dat <- data.frame(   x = factor(letters[1:5], levels = letters[5:1]),   y = 1:5 )  # With rtables layout functions basic_table() %>%   split_cols_by(\"x\", ref_group = \"c\", split_fun = ref_group_position(\"last\")) %>%   analyze(\"y\") %>%   build_table(dat) #>         e      d      b      a      c   #> ——————————————————————————————————————— #> Mean   5.00   4.00   2.00   1.00   3.00  # With tern layout funcitons adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(\"first\")) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM B          ARM A          ARM C     #>                             (N=73)         (N=69)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     23.9           32.0           20.8     #>     95% CI               (18.3, 32.9)   (22.5, 49.3)   (12.9, 26.0) #>   25% and 75%-ile         9.8, 42.0      17.4, 65.3     7.3, 37.1   #>   Range                  0.1 to 154.1   0.3 to 155.5   0.6 to 80.7   basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(2)) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     95% CI               (22.5, 49.3)   (18.3, 32.9)   (12.9, 26.0) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   # level_order -------- # Even if default would bring ref_group first, the original order puts it last basic_table() %>%   split_cols_by(\"Species\", split_fun = level_order(c(1, 3, 2))) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94     # character vector new_order <- level_order(levels(iris$Species)[c(1, 3, 2)]) basic_table() %>%   split_cols_by(\"Species\", ref_group = \"virginica\", split_fun = new_order) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-6-9005","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6.9005","text":"Fixed bug a_summary() causing non-unique row_name values occur multiple statistics selected count variables.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-096","dir":"Changelog","previous_headings":"","what":"tern 0.9.6","title":"tern 0.9.6","text":"CRAN release: 2024-09-24","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6","text":"Added errorbar_width linetype parameters g_lineplot. Added .formats argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users specify formats. Added riskdiff argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users add risk difference table column, function control_riskdiff specify settings risk difference column. Added warning tabulate_rsp_subgroups pval statistic selected df correctly generated add p-values output table. Added n_rate statistic non-default option estimate_incidence_rate returns number events observed estimated incidence rate. Added n_unique statistic non-default option estimate_incidence_rate returns total number patients least one event observed. Refactored estimate_incidence_rate work analyze function summarize function, controlled added summarize parameter. summarize = TRUE, labels can fine-tuned via new label_fmt argument function. Added fraction statistic analyze_var_count method group. Improved summarize_glm_count() documentation associated functions better describe results functions’ purpose. Added method argument s_odds_ratio() estimate_odds_ratio() control whether exact approximate conditional likelihood calculations used.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-6","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6","text":"Added defaults d_count_cumulative parameters described documentation. Fixed bug empty levels g_lineplot x-axis shown either plots. Fixed bug a_surv_time threw error split \"is_event\". Fixed disappearing line g_lineplot using one group strata level. Fixed defaults formats labels get_formats_from_stats get_labels_from_stats. Fixed bug linear scaling factor (scale parameter) applied response rate h_glm_count distributions logarithmic link function. Fixed bug decorate_grob handle well empty strings NULL values title footers. Fixed bug g_km caused error multiple records data estimates max time. Fixed issue wrong wrapping due different \\n vector behavior cope well split_string().","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6","text":"Began deprecation confusing functions summary_formats summary_labels. Enhanced general descriptions analyze summarize functions throughout package documentation. Finalized deprecation strata cohort_id arguments g_lineplot. Moved incidence rate helper functions separate h_incidence_rate.R file.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-095","dir":"Changelog","previous_headings":"","what":"tern 0.9.5","title":"tern 0.9.5","text":"CRAN release: 2024-06-21","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.5","text":"Added facet_var g_lineplot allow plot faceting factor variable. Added examples tests label_all parameter extract_survival_biomarkers extract_survival_subgroups. Added xticks, xlim, ylim arguments g_lineplot allow customization x y axes. Updated g_lineplot legend follow factor levels set users.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.5","text":"Fixed bug s_ancova prevented statistics printed arm levels include special characters. Fixed bug decorate_grob prevented right margins respected adding title footers decorations.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.5","text":"Began deprecation unused label_all parameter tabulate_survival_biomarkers tabulate_survival_subgroups, redirection parameter associated extract_* functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-094","dir":"Changelog","previous_headings":"","what":"tern 0.9.4","title":"tern 0.9.4","text":"CRAN release: 2024-04-17","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.4","text":"Added h_glm_negbin h_glm_count enable count data analysis using negative binomial model. Added argument grade_groups_only count_occurrences_by_grade allow users display rows specified grade groups. Added internal function df2gg converts data.frame objects ggplot objects. Added functions control_surv_med_annot control_coxph_annot configure g_km annotation table sizes/positions. Refactored g_km output ggplot object instead grob object. Refactored g_forest output ggplot object instead grob object.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.4","text":"Default format mean p-values (mean_pval) updated \"xx.xx\" \"x.xxxx | (<0.0001)\".","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.4","text":"Fixed nested column split label overlay issue rtable2gg clean appearance text labels. Fixed bug s_ancova causing incorrect difference calculations arm variables irregular levels. Fixed bug format_count_fraction_fixed_dp print fraction 1 (100%). Fixed bug g_lineplot causing default labels update according specified control settings. Fixed bug causing error automatic value formatting applied NA values.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.4","text":"Added function expect_snapshot_ggplot test setup file process plot snapshot tests allow plot dimensions set. Adapted argument renames introduced ggplot2 3.5.0. Renamed individual_patient_plot.R g_ipp.R. Removed instances deprecated parameters time_unit_input, time_unit_output, na_level indent_mod. Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, summary_custom. Removed vdiffr package Suggests DESCRIPTION file. Began deprecation named element strat, renamed strata, within variables argument h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, extract_survival_subgroups. Began deprecation strat argument s_coxph_pairwise replaced strata argument. Began deprecation forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, grid.forest functions. Began deprecation longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, h_grob_coxph. Began deprecation grob/grid related functions stack_grobs, arrange_grobs, draw_grob longer used tern.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-093","dir":"Changelog","previous_headings":"","what":"tern 0.9.3","title":"tern 0.9.3","text":"CRAN release: 2023-12-08","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.3","text":"Added ref_group_position function place reference group facet last, first certain position. Added keep_level_order split function retain original order levels split. Added level_order split function reorder manually levels. Added function get_indents_from_stats format return indent modifiers given set statistics. Added internal utility function apply_auto_formatting check \"auto\" formats replace implementation format_auto analyze functions. Added utility function labels_use_control modify labels control specifications. Added list containing default statistics method group, tern_default_stats. Added summarize function version count_occurrences analyze function, summarize_occurrences. Added referential footnotes surv_time censored range observations, controlled via ref_fn_censor parameter. Added helper function h_adlb_abnormal_by_worst_grade prepare ADLB data use input count_abnormal_by_worst_grade. Added s_bland_altman function assess agreement two numerical vectors. Added function rtable2gg converts rtable objects ggplot objects. Added helper function set default na_str globally set_default_na_str() added default_na_str() interested functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.3","text":"Added ref_group_coxph parameter g_km specify reference group used pairwise Cox-PH calculations annot_coxph = TRUE. Added annot_coxph_ref_lbls parameter g_km enable printing reference group table labels annot_coxph = TRUE. Added x_lab parameter g_lineplot customize x-axis label. Remove 25% padding y-axis g_lineplot. Added support creating multiple risk difference columns, comparing single comparison group. Multiple comparison groups can specified vector via arm_y argument. Allowed numeric vector count_by input analyze_num_patients summarize_num_patients. Aligned plot table vertically g_lineplot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.3","text":"Fixed bug decorate_grob preventing text wrapping accounting font size. Fixed implementation na_str argument column-wise analysis tabulation functions.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.3","text":"Specified minimal version package dependencies. Upgraded to_string_matrix take account widths printing parameters.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.2","text":"Added na_str argument analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.2","text":"Added formatting function format_count_fraction_lt10 formatting count_fraction special consideration count less 10. Updated s_summary.logical output count_fraction denominator zero display NA instead 0 tables. Updated analyze_vars_in_cols allow character input indicate whether nominal time point post-dose pre-dose applying 1/3 imputation rule.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.2","text":"Fixed bug g_km causing error converting certain annotation width units.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.2","text":"Began deprecation na_level argument s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, summarize_coxreg replaced na_str argument. strata cohort_id parameters renamed group_var subject_var respectively g_lineplot control_lineplot_vars .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.1","text":"Added imputation_rule function apply imputation rule data. Added new format function format_sigfig allow numeric value formatting specified number significant figures. Added vectors containing default statistic formats labels tern_default_formats tern_default_labels, respectively. Added function get_stats return methods given statistical method groups. Added function get_formats_from_stats return formats get_labels_from_stats return labels given set statistics. Added \"auto\" option .formats. uses format_auto determine automatically number digits. Added title argument h_grob_tbl_at_risk annot_at_risk_title argument g_km h_km_layout allows user add “Patients Risk” title Kaplan-Meier risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.1","text":"Refactored tabulate_rsp_subgroups pass sanitation checks preventing creation degenerate subtables. Updated analyze_vars_in_cols use caching, allow implementation imputation rule via imp_rule argument, allow user specify cell alignment via .aligns argument. Updated add_rowcounts allow addition row counts alt_counts_df using alt_counts argument. Added gp argument g_forest control graphical parameters font size.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.1","text":"Grouped functions relating valid method names default formats labels new source file utils_defaults_handling.R. Started deprecation summary_custom() a_summary() S3 method. Renamed statistical method p-value discrete case pval_counts. Removed a_summary_internal() favor one main a_summary().","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-090","dir":"Changelog","previous_headings":"","what":"tern 0.9.0","title":"tern 0.9.0","text":"CRAN release: 2023-09-01","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.0","text":"Added stat_propdiff_ci function calculate proportion/risk difference CI. Added risk difference column functionality via riskdiff argument functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, summarize_num_patients.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.0","text":"Refactored function a_summary longer use helper function create_afun_summary. Refactored functions summarize_vars compare_vars use refactored a_summary function. Created new internal helper functions ungroup_stats ungroup statistics calculated factor variables, a_summary_internal perform calculations a_summary.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.0","text":"Fixed bug s_count_occurrences_by_grade “missing” grade always appears final level. Fixed bug analyze_vars_in_cols categorical data used. Fixed bug s_count_occurrences_by_grade levels relabeled reordering account “missing” grades.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.0","text":"Fixed swapped descriptions .N_row .N_col parameters. Removed internal calls df_explicit_na. Changes NA values happen externally tern functions, depending users’ needs. Reinstated correct soft deprecation create_afun_summary create_afun_compare.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.5","text":"Added ylim argument g_km allow user set custom limits y-axis. Added assertion g_km checks whether one arm present data annot_coxph true. Added flag_labels argument s_count_patients_with_flags enable label handling options count_patients_by_flags. Added nested argument analyze wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, estimate_incidence_rate, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, analyze_num_patients, coxph_pairwise, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.5","text":"Started deprecation cycle summarize_vars control_summarize_vars. Renamed analyze_vars control_analyze_vars reflect underlying rtables machinery keeping backward compatibility aliases.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-084","dir":"Changelog","previous_headings":"","what":"tern 0.8.4","title":"tern 0.8.4","text":"CRAN release: 2023-06-27","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.4","text":"Added method character class h_coxreg_inter_effect enabling character covariates summarize_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.4","text":"Began deprecation time_unit_input time_unit_output arguments replaced input_time_unit num_pt_year, respectively, control_incidence_rate. Removed deprecated pairwise function. Deprecated a_compare replaced a_summary argument compare = TRUE. Deprecated helper functions create_afun_summary create_afun_compare longer used a_summary a_compare respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.4","text":"Fixed long double assertion check sum(weights) M1mac installation.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-083","dir":"Changelog","previous_headings":"","what":"tern 0.8.3","title":"tern 0.8.3","text":"CRAN release: 2023-06-19","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.3","text":"Added explicit zero counts g_km plot “risk” annotation tables. Added flag total level split analyze_patients_exposure_in_cols. Implemented .indent_mods argument functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, cfun_by_flag. Updated summarize_coxreg print covariates data rows univariate Cox regression interactions content rows otherwise. Removed “baseline status” text d_count_abnormal_by_baseline labels. Improved default sizing annotation tables g_km added dynamic scaling surv_med coxph annotation tables, customization via width_annots argument.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.3","text":"Fixed bug split_text_grob preventing titles footnotes properly formatted printed decorate_grob. Fixed bug g_lineplot preventing addition lines plot midpoint statistic calculations result NA value(s). Fixed tern:::tidy.glm formals respect broom:::tidy.default formals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.3","text":"Updated README include installation instructions CRAN. Remove examples unexported functions. Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport. Updated README include installation instructions CRAN. Began deprecation indent_mod argument replaced .indent_mods argument summarize_num_patients analyze_num_patients.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"breaking-changes-0-8-2","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"tern 0.8.2","text":"Refactored s_coxreg summarize_coxregto work new analysis function a_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.2","text":"Added section_div na_level arguments summarize_vars. Added median_range numeric variable statistic option summarize_vars. Corrected ordering factor levels d_onco_rsp_label. Added new “Analyze Functions”, “Summarize Functions”, “Analyze Functions Columns” overview pages. Consolidated KM plot documentation within g_km function. Added a_count_patients_sum_exposure summarize_patients_exposure_in_cols new analyze function analyze_patients_exposure_in_cols. Added informative error user selects invalid method unstratified analyses s_proportion_diff. Updated s_summary s_compare allow NA values input variables. factor variables NAs, na.rm = FALSE explicit NA level automatically added. na.rm = TRUE also consider \"<Missing>\" values exclude . Updated purpose na_level parameter s_summary s_compare align tern functions. Instead string consider NA setting na.rm = TRUE, now defines string print place NA values output table.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.2","text":"Fixed missing label TRTEDTM tern datasets. Fixed improper implementation na_level argument summarize_vars preventing effect.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.2","text":"Implemented lubridate package date variables tern datasets. Organized .gitignore .Rbuildignore files. Removed deprecated footnotes functions related files. Started deprecation cycle pairwise function. Moved count_patients_with_flags functions count_patients_with_event.R count_patients_with_flags.R.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-8-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.0","text":"Added summarize_glm_count function analyze count data using linear model. Added legend g_step. Added formatting functions format_fraction_fixed_dp format_count_fraction_fixed_dp fixed single decimal place percentages. Added na_level labelstr arguments summarize_vars_in_cols. Added analyze_num_patients include summary beginning repeat paginating. Added h_row_first_values function general helper function retrieve first values specific rows. Added option remove \"(n)\" suffix unique_count labels s_num_patients. Added options g_km annotate statistics (annot_stats) add corresponding vertical lines (annot_stats_lines).","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-8-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.0","text":"Fixed bug causing incorrect ordering numeric grade levels missing grades present s_count_occurrences_by_grade. Refactored summarize_vars_in_cols work pagination machinery. Fixed bug allow passing conf_level argument emmeans::contrast() s_ancova. Fixed bugs rtables_access.R caused checking specific combinations (also standard values never used) column indices names. Fixed single applicable record bug count_abnormal_by_grade. Fixed bug add_rowcounts caused row count row values count zero. Fixed bug h_col_indices causing error pruning combination columns. Fixed bug test_proportion_diff missing argument var_labels.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-tests-0-8-0","dir":"Changelog","previous_headings":"","what":"Documentation and Tests","title":"tern 0.8.0","text":"Added tests increase code coverage. Created separate documentation files functions different sections pkgdown reference. Created separate .R files logistic regression cox regression helper functions. Fixed table tests using analyze_num_patients generate initial summary repetition paginating. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Updated summarize_ancova examples use iris dataset instead scda data. Created vignette saves cached synthetic CDISC dataset files data/ folder generated cached synthetic datasets. Updated examples/tests use datasets data/ folder instead scda datasets. Removed template tests tern. tests internal repo scda.test.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-8-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.0","text":"Renamed summarize_vars_in_cols analyze_vars_in_cols reflect appropriate analyze logic. Removed redundant summary_in_cols helper functions. Exported function format_xx. Replaced deprecated ggplot2 functions/arguments fix warnings. Replaced deprecated function forcats::fct_explicit_na forcats::fct_na_value_to_level. Removed deprecated wrap_text function related files. Started deprecation cycle footnotes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.10","text":"Added stratified Newcombe stratified Wilson statistics estimate_proportion estimate_proportion_diff relative tests. Added stat_mean_pval, new summary statistic calculate p-value mean. Added statistic mean_se (mean standard error) summarize_variables related functions. Introduced Rdpack references.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.10","text":"Redesign data handling tests removing repetitive data loads library calls. Added DescTools::BinomDiffCI function within tern. Added new parameter summarize_logistic specify pivoted value use analysis. Updated s_coxph_pairwise generate log-rank p-value using original log-rank test instead Cox Proportional-Hazards Model. Implemented nestcolor examples adapting g_km, g_ipp, g_waterfall, g_step, g_lineplot, g_forest. Added parameters interaction_y interaction_item ANCOVA make interaction calculations available. Added new parameter footnotes add footnotes g_km.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"migration-from-assertthat-to-checkmate-0-7-10","dir":"Changelog","previous_headings":"","what":"Migration from assertthat to checkmate","title":"tern 0.7.10","text":"Implemented checkmate::assert_vector, checkmate::assert_set_equal, checkmate::assert_int check vector type, length, values. Replaced standard assertions checkmate following functions: all_elements_in_ref, is_df_with_nlevels_factor, is_df_with_no_na_level, is_proportion_vector, is_quantiles_vector, is_character_or_factor, is_nonnegative_count, is_valid_character, assert_character_or_factor, assert_equal_length has_tabletree_colnames. Modified is_proportion, is_equal_length, is_df_with_no_na_level, is_df_with_nlevels_factor, is_variables, is_df_with_variables, is_df_with_factors, is_valid_factor use assertion logic. Added verbose warnings as_factor_keep_attributes. Made assert_df_with_factors assert_proportion_value internal functions. Renamed assertthat.R test-assertthat.R utils_checkmate.R test-utils_checkmate.R.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-namespace-polishing-0-7-10","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE Polishing","title":"tern 0.7.10","text":"count_abnormal_by_marked (reference abnormal_by_marked), count_abnormal_lab_worsen_by_baseline h_adlb_worsen (reference abnormal_by_worst_grade_worsen_from_baseline), count_abnormal_by_worst_grade (reference abnormal_by_worst_grade), to_string_matrix, tidy.summary.coxph, tidy.step, surv_timepoint, (reference survival_timepoint), surv_time (reference survival_time), coxph_pairwise (reference survival_coxph_pairwise), extract_survival_subgroups tabulate_survival_subgroups (reference survival_duration_subgroups), extract_survival_biomarkers tabulate_survival_biomarkers (reference survival_biomarkers_subgroups), control_summarize_vars, s_summary a_summary (reference summarize_variables) kept S3 method tree. summarize_patients_exposure_in_cols, summarize_num_patients s_num_patients, s_num_patients_content, summarize_num_patients. count_cumulative, count_missed_doses, count_patients_events_in_cols, summarize_colvars, summarize_change, summarize_ancova,.rtable, color_palette, add_footnotes. (statistical function controls) control_coxreg, control_coxph, control_incidence_rate, control_lineplot_vars, control_surv_time, control_surv_timepoint, control_logisitic, control_step. stat_mean_ci, stat_median_ci, split_cols_by_groups, explicit_na, sas_na, extract_rsp_subgroups, tabulate_rsp_subgroups, extract_rsp_biomarkers, tabulate_rsp_biomarkers, keep_rows, keep_content_rows, has_count_in_any_col, has_fraction_in_cols, has_fraction_in_any_col, has_fractions_difference, test_proportion_diff, pairwise, logistic_regression, estimate_incidence_rate, control_incidence_rate (reference incidence_rate), cut_quantile_bins, estimate_multinomial_rsp, decorate_grob_set, extreme_format, fit_rsp_step, fit_survival_step, footnotes, footnotes-set, format_count_fraction, format_fraction_threshold, formatting_functions, format_fraction, combination_function (S4 method), compare_variables (S3 method), kaplan_meier. (chain functions, reference abnormal_by_marked) s_count_abnormal_by_marked, a_count_abnormal_by_marked. (chain functions, reference abnormal_by_worst_grade_worsen_from_baseline) a_count_abnormal_lab_worsen_by_baseline, s_count_abnormal_lab_worsen_by_baseline. (chain functions, reference abnormal_by_worst_grade) s_count_abnormal_by_worst_grade, a_count_abnormal_by_worst_grade. (chain functions, reference survival_timepoint) s_surv_timepoint, s_surv_timepoint_diff, a_surv_timepoint, a_surv_timepoint_diff. (chain functions, reference survival_time) s_surv_time, a_surv_time. (chain functions, reference survival_coxph_pairwise) s_coxph_pairwise, a_coxph_pairwise. (chain functions, reference survival_duration_subgroups) a_survival_subgroups. (chain functions, reference count_cumulative) s_count_cumulative, a_count_cumulative. (chain functions, reference count_missed_doses) s_count_nonmissing, s_count_missed_doses, a_count_missed_doses. (chain functions, reference count_patients_events_in_cols) s_count_patients_and_multiple_events, summarize_patients_events_in_cols. (chain functions, reference incidence_rate) s_incidence_rate, a_incidence_rate. (cox regression helper) cox_regression_inter, decorate_grob_factory, draw_grob, estimate_coef. summary_labels, summary_formats, s_count_patients_sum_exposure, a_change_from_baseline s_change_from_baseline, a_ancova, s_ancova, arrange_grobs, as_factor_keep_attributes, combine_levels, split_text_grob, groups_list_to_df, s_cox_multivariate, is_leaf_table, a_response_subgroups, range_noinf, has_count_in_cols, has_counts_difference, prop_chisq, prop_cmh, prop_schouten, prop_fisher, s_test_proportion_diff, a_test_proportion_diff, fct_discard, fct_explicit_na_if.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.10","text":"Fixed retrieval method stats::ancova output due version inconsistency. Fixed tests respect new standard print NA coming rtables. Fixed error tests coming changes formatters::var_labels. Fixed prop_diff functions respect success responses (TRUE values). Fixed error coming comparing factors vector characters vector. Fixed empty vector exception cut_quantile_bins. Fixed exception error empty strings present pivoted columns (rtables split functions) Fixed bug s_ancova causing error first level arm factor control arm. Fixed bug s_abnormal_by_worst_grade one PARAM level. Fixed bug prop_diff_wald selecting responders, updated tests accordingly. Fixed bug h_ancova caused error deselecting covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.10","text":"Added deprecated badge g_mmrm. Removed internal function calls examples (tern:::) added dontrun internal function examples. Removed warnings messages console occurring examples tests. Deprecated functions color_palette h_set_nest_theme favor nestcolor::color_palette nestcolor::theme_nest, respectively. Removed deprecated functions: color_palette, color_palette_core, h_set_nest_theme, s_cox_univariate. Removed deprecated MMRM functions: fit_mmrm, g_mmrm_diagnostic, g_mmrm_lsmeans, .rtable.mmrm, h_mmrm_fixed, h_mmrm_cov, h_mmrm_diagnostic, tidy.mmrm, s_mmrm_lsmeans, s_mmrm_lsmeans_single, summarize_lsmeans. Renamed functions arm study_arm extract extract_by_name. Renamed rtables.R utils_rtables.R. Extracted cox_regression_inter separate file cox_regression. Renamed estimate_incidence_rate.R incidence_rate.R match documentation grouping name. Extracted control_incidence_rate separate file produces separate documentation file. Added @md removed @order incidence_rate.R. Modified examples accordingly. Removed hyperlink prop_schouten function documentation. Exported draw_grob function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"fix-0-7-8","dir":"Changelog","previous_headings":"","what":"Fix","title":"tern 0.7.8","text":"h_split_by_subgroups documentation warning fix wrong placing example block","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"documentation-and-namespace-polishing-0-7-8","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE polishing","title":"tern 0.7.8","text":"Adopting standard badges @description instead every @descriptionIn function. Corrected accordingly summarize_variables_in_cols Added stable badge g_lineplot, g_step, g_waterfall, cox_regression, score_occurrences, add_rowcounts, odds_ratio, count_occurrences, count_occurrences_by_grade, explicit_na, df_explicit_na, count_patients_with_event, decorate_grob, combine_groups, append_varlabels, univariate, stack_grobs, count_abnormal (reference abnormal), count_abnormal_by_baseline (reference abnormal_by_baseline). (helper functions) h_format_row, h_map_for_count_abnormal (utils functions) make_names, month2day, day2month empty_vector_if_na, aesi_label, n_available, format_xx, arm. count_values_funs, prop_difference, combine_counts. (chain functions) s_count_abnormal, a_count_abnormal. (chain functions) s_count_abnormal_by_baseline, a_count_abnormal_by_baseline, d_count_abnormal_by_baseline. Deprecated s_cox_univariate function now deprecated badge.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.8","text":"Enhanced g_lineplot table automatically scale table height return ggplot object. Enhanced g_ipp caption argument adjust position. Enhanced prop_diff, tern function related functions able apply continuity correction Newcombe method. Enhanced summarize_numeric_in_columns summarize_variables allow factor/character summary able summarize number BLQs AVALC ADPC dataset. Updated order summarize variables stats manual order consistency. Added sum option summarize_variables. Use consistent color palette plotting (stream default). Enhanced h_pkparam_sort function argument key_var allow data different column names.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.8","text":"Updated test-table_aet02.R variant 12. Changed scda data version ‘2022-02-28’. Added template pkgdown site. Removed package dependencies grDevices, stringr, viridisLite. Renaming summarize_numeric_in_columns summarize_variables_in_columns. Renaming summarize_vars_numeric_in_cols summarize_vars_in_cols. Fixed bug points g_lineplot plot connected missing values. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"breaking-changes-0-7-7","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"tern 0.7.7","text":"Move MMRM separate package tern.mmrm.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-7","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.7","text":"Added h_pkparam_sort order PK PARAM value based order dataset generated d_pkparam(). Added d_pkparam generate PK parameter map sorting.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.7","text":"Changed nudge_y argument h_g_ipp dependent data, fixing issue whereby baseline labels offset incorrectly. Enhanced stat_mean_ci s_summary.numeric calculate geometric mean confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.7","text":"Updated dependencies internal adjustments rtables package refactor. Removed with_label, var_labels, var_labels<- resolve conflict formatters package, new dependency. Added new “Introduction tern” “tern tabulation” vignettes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-6","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.6","text":"Added h_map_for_count_abnormal create map used trim_levels_to_map split function calling helper function. supports two methods: one observed mapping, one least low limit zero least one non missing high limit. Added s_summary_numeric_in_cols summarize_vars_numeric_in_cols functions generate summary statistics columns, mainly used PK datasets. Added five statistics s_summary.numeric use s_summary_numeric_in_cols.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.6","text":"Enhanced functions tabulate_survival_subgroups tabulate_rsp_subgroups (Survival Duration Best Response analyses) calculate N-s based records considered create model. Enhanced function estimate_proportion related functions able apply continuity correction Wilson method. Refactored count_abnormal_by_marked related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal_by_worst_grade related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal function related statistics formatting functions use efficient layout trim_levels_to_map split function split_rows_by show desired levels table. Also updated abnormal argument able consider one level direction. breaking change. Enhanced function estimate_incidence_rate related functions consider week time unit data input.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"tern 0.7.6","text":"Fixed bug assertthat functions output wrong data frame names limited length failure message outputs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.6","text":"Removed dependency utils.nest using checkmate purrr packages validation moved get_free_cores skip_if_too_deep functions utils.nest tern.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-5","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.5","text":"Added functions estimate continuous biomarker effects across subgroups survival binary response endpoints, used produce corresponding forest plots, see survival_biomarkers_subgroups response_biomarkers_subgroups. Added g_lineplot plot function, including new h_format_row helper function control_lineplot_vars function. Removed g_summary_by. Added new safety helper function h_stack_by_baskets stack events SMQ /CQ basket flag ADAE data set.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.5","text":"Added couple new statistics s_summary.numeric. Added names attribute element final list returned s_summary.numeric function. Added summary_formats summary_labels helper functions. Added option also convert logical variables factor variables df_explicit_na. Refactored h_append_grade_groups improve flexibility, robustness clearness, make sure result ordering according order grade_groups. Also, added remove_single argument controls whether elements one-element grade groups output removed. Added var_labels show_labels arguments count_occurrences count_patients_with_flags allow creation title row. Added na_level argument count_abnormal_by_baseline. Updated h_append_grade_groups longer fill-empty grade groups zeros.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.5","text":"Fixed prop_diff_cmh handle edge case FALSE (TRUE) responses. Enhanced g_mmrm_diagnostic improve error handling data amenable Locally Weighted Scatterplot Smoothing. Plot can now display combination annotation tables number patients risk, median survival time, Cox-PH summary. Function return warning instead error arm variable includes single level annot_coxph = TRUE. Lines plot now start time 0 probability 1. Category labels can include equals sign.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.5","text":"Fixed day2month month2day work NA data. Added parameters stat_mean_ci stat_median_ci may return different outputs. Added functionality h_row_counts handle analysis rows NULL cells. Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-4","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.4","text":"count_abnormal_by_marked tabulates marked laboratory abnormalities. summarize_patients_exposure_in_cols tabulates patient counts sum exposure across patients.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.4","text":"Enhanced MMRM-related functions fitting models without arm variable. Updated cox_regression work without covariates. Also case interaction model summary, p-values main effect coefficients longer displayed. Descriptive statistics returned summarize_vars now include quantiles. summarize_vars now accepts control function control_summarize_vars specify details confidence level mean median quantile details. control argument replaces conf_level. Added var_labels show_labels arguments count_occurrences_by_grade. Changed indent argument append_varlabels accept non-negative integer represent indent space defined user. Previous calls Boolean indent integer conversion produce warning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.4","text":"Corrected tabulate_survival_subgroups related survival forest plot functions use total number events, instead observations, default scaling symbol sizes plot. (user might still use total number observations manually wish .) Helper function h_adsl_adlb_merge_using_worst_flag now impute BTOXGR missing visits.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.4","text":"Deleted count_abnormal_by_worst_grade_by_baseline related statistic analysis functions simpler design create lab abnormality tables. Switched data examples use scda instead random.cdisc.data package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-features-0-7-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.3","text":"Added Subgroup Treatment Effect Pattern (STEP) model fitting functions fit_rsp_step fit_survival_step, corresponding tidy method tidy.step well graph function g_step. Added new layout function compare_vars compares variables different types columns produces p-value comparison reference column. Function built top summarize_vars functionality. cut_quantile_bins cuts numeric vector quantile bins. fct_collapse_only collapses levels factor keeps order provided. fct_explicit_na_if inserts explicit missings factor based condition. range_noinf kind wrapper function base::range. returns c(NA, NA) instead c(-Inf, Inf) zero-length data.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"enhancements-0-7-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.3","text":"Cox regression via fit_coxreg_univar fit_coxreg_multivar now also possible without treatment arm. univariate case means fits separate univariate models provided covariates tabulation corresponding effect estimates can later occur. Added fraction result returned s_count_occurrences. contains list numerators denominators one element per occurrence. Updated sum_num_patients count_occurrences result unique count_fraction return (0, 0) input empty. Added new argument groups_lists extract_survival_subgroups, extract_rsp_subgroups associated helper functions allows group factor levels subgroup variables manually defined groups, enhancing flexibility resulting forest graphs. Forest graph function g_forest now extracts default arguments attributes input table produced tabulate_rsp_subgroups tabulate_survival_subgroups user manually anymore. Remove arm variable name arm labels plot legend annotation tables. Show symbol used mark censored cases match order arm variable factor levels legend. Display hazard ratio confidence interval two decimal places. Updated default position hazard ratio table stay left bottom corner x-axis. Use arm value strata name treatment arm variable single level. Updated s_surv_time function use newly created function range_noinf instead base::range. New argument no_fillin_visits added h_adsl_adlb_merge_using_worst_flag specify excluded visits post-baseline worst toxicity grade output. Improved h_adsl_adlb_merge_using_worst_flag include variables shared adsl adlb, along PARAM, PARAMCD, ATOXGR, BTOXGR optionally AVISIT, AVISITN by_visit = TRUE. Prior output contained USUBJID, ARMCD, PARAMCD, ATOXGR, BTOXGR.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"bug-fixes-0-7-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.3","text":"Fix bug s_surv_timepoint cases zero patients risk. Modified stat_median_ci function passing empty var empty name, row names contain missing values error show.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"miscellaneous-0-7-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.3","text":"Deprecated s_cox_univariate function, use fit_coxreg_univar function instead. Updated default formats hr hr_ci a_coxph_pairwise median s_surv_time align STREAM. Updated pre-processing code files test-table_ttet01.R test-table_dort01.R make sure analysis variable EVNT1 levels factor defined. Improved error message number levels factor variable data frame expected.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-072","dir":"Changelog","previous_headings":"","what":"tern 0.7.2","title":"tern 0.7.2","text":"Fixed column label internal test errors.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-071","dir":"Changelog","previous_headings":"","what":"tern 0.7.1","title":"tern 0.7.1","text":"New argument position_surv_med added g_km move position annotation table median survival times. Fixed bug g_km related ignored arguments pch size passed helper function h_ggkm. Updated xticks max_time arguments g_km greater functionality. max_time added argument h_xticks allow . Fixed bug prop_diff_cmh led NaN weighted proportion difference estimates missing confidence intervals. change, including patients one treatment arm least one stratum estimation lead numeric results. Fixed bug prop_cmh giving error case least one stratum containing less two observations. New argument n_events added estimate_incidence_rate. New argument denom added count_occurrences. New arguments yval ci_ribbon added g_km. Add new individual patient plot function g_ipp along helpers h_g_ipp h_set_nest_theme. Fixed bug count_patients_with_events, now shows zero counts without percentage. Fixed bug get_mmrm_lsmeans allow MMRM analysis 3000 observations. Updated stat_mean_ci stat_median_ci handle edge cases number elements input series equal 1. cases, NA_real_ now returned, instead NA +/-Inf confidence interval (CI) estimates. Rename n_lim argument stat_mean_ci n_min better reflect desired meaning.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-070","dir":"Changelog","previous_headings":"","what":"tern 0.7.0","title":"tern 0.7.0","text":"version tern introduces major rewriting tern due change layout based tabulation rtables. tern now build tables directly anymore, instead provides analysis functions build tables, see examples. * Counting patients abnormal values post-baseline count_abnormal. * Counting patients graded abnormal values count_abnormal_by_worst_grade. * Counting patients abnormal values baseline status count_abnormal_by_baseline. * Counting patients missed doses s_count_missed_doses count_missed_doses. * Counting patients event flags count_patients_with_event count_patients_with_flags. * Summarizing variables summarize_vars (supports numeric, factor, character logical variables). Note factors need NAs converted na_level use. * Summarizing change baseline summarize_change. * Summarizing variables columns summarize_colvars. * Estimating difference responder proportions estimate_proportion_diff. * Estimating difference Odds Ratio estimate_odds_ratio. * Testing difference responder proportions test_proportion_diff. * Estimating responder proportion level factor estimate_multinomial_response. * Fitting tabulating results Cox regressions fit_coxreg_univar, fit_coxreg_multivar summarize_coxreg, respectively. * Pruning occurrence tables (tables counts fractions) flexible rules, see ?prune_occurrences details. * Sorting occurrence tables using different options, see ?score_occurrences details. * Fitting tabulating MMRM models fit_mmrm .rtable summarize_lsmeans, see ?tabulate_mmrm details. * Counting number unique non-unique patients summarize_num_patients. * Counting occurrences count_occurrences. * Counting occurrences grade summarize_occurrences_by_grade count_occurrences_by_grade. * Counting patients events columns summarize_patients_events_in_cols. * Tabulating binary outcome response subgroup extract_rsp_subgroups tabulate_rsp_subgroups. * Tabulating survival duration subgroup extract_survival_subgroups tabulate_survival_subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-069","dir":"Changelog","previous_headings":"","what":"tern 0.6.9","title":"tern 0.6.9","text":"Removing used imports.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-068","dir":"Changelog","previous_headings":"","what":"tern 0.6.8","title":"tern 0.6.8","text":"Improved handling missing data aggregation functions: a_mean_sd, a_median, a_n_true_and_freq, a_count, a_q1q3, a_iqr, a_range. New default p-value method s_test_proportion_diff: Chi-Squared Test Schouten Correction. Add new function t_contingency contingency tables. Renamed class splitText dynamicSplitText resolve name conflict package ggpubr. Add rreplace_format tabulation post-processing. Add new tern function t_ancova create ANCOVA tables, well corresponding elementary table function t_el_ancova summary function s_ancova. Add new tern function s_odds_ratio estimate Odds Ratio response categories, well corresponding elementary table function t_el_odds_ratio. Added new CI methods (agresti-coull, jeffreys) s_proportion. Added new CI methods anderson-hauck newcombe s_proportion_diff. Added new p-value methods (Fisher’s Exact, Chi-Squared Test Schouten Correction) s_test_proportion_diff. binary summary table function t_binary_outcome takes now lists (instead character vectors) specified helper function control_binary_comparison arguments strat_analysis unstrat_analysis. Odds Ratio estimates CIs now removable included default, similarly subsections arm comparison analyses. Also added argument rsp_multinomial. Add new table function t_el_multinomial_proportion. Add new table function t_abn_shift. Add new MMRM analysis function s_mmrm, well corresponding table functions t_mmrm_lsmeans, t_mmrm_cov, t_mmrm_diagnostic, t_mmrm_fixed, plot functions g_mmrm_lsmeans, g_mmrm_diagnostic. results match SAS results (numeric precision). Deprecated old MMRM functions a_mmrm t_mmrm (give deprecation warning still work) remove next release. reason results functions don’t match SAS results. Fix bug g_km related numbers patients risk table correct numbers integer time--event variable inputs.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-067","dir":"Changelog","previous_headings":"","what":"tern 0.6.7","title":"tern 0.6.7","text":"functions row_by argument, inputs longer require use nested_by. Add stat_mean_ci stat_median_ci error bars ggplot2. Add new tern function t_coxreg single interface diverse cox regression types. Add compound table binary endpoint: t_binary_endpoint elementary functions: t_el_proportion, t_el_proportion_diff t_el_test_proportion_diff. supporting summary functions added : s_proportion, s_adj_proportion_diff, s_proportion_diff s_test_proportion_diff. Added new tern function t_events_patyear create event table adjusted person-years. Added new tern function t_abnormality elementary table function t_el_abnormality. Removed grade_levels argument t_events_term_grade_id functions. Post-processing reordering leaves table tree creates different ordering rows required. Creating helper function occur later time. Added prune_zero_rows argument t_events_per_term_grade_id t_max_grade_per_id show rows zeros can clutter visualization Shiny app make slower. Fixed position (N=xx) t_summary_by output summarizing numeric columns parallel compare_in_header. Rename t_coxph t_coxph_pairwise reflect model process, add details documentation. Remove test.nest dependency. Keep column labels splitting data tree.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-066","dir":"Changelog","previous_headings":"","what":"tern 0.6.6","title":"tern 0.6.6","text":"Remove test.nest dependency.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-065","dir":"Changelog","previous_headings":"","what":"tern 0.6.5","title":"tern 0.6.5","text":"Change default option denominator N t_summary. Fix IQR bug: IQR Q3 minus Q1. Add new function t_logistic multi-variable logistic regression table. Add new function df_explicit_na replace NA explicit values. Added possibility t_tte specify confidence level independent survfit, coxph, ztest, see manual. Fixed bug t_rsp showing p-value, odds ratio CIs strata_data NULL. Added stratified analysis t_forest_rsp t_forest_tte, footnotes g_forest. Added footnotes, footnotes<- add_footnotes<- functions deal footnotes. Added argument conf_int confidence interval level t_el_forest_rps, t_forest_rsp, t_el_forest_tte, t_forest_tte. Added argument col_symbol_size g_forest control relative size symbols used plot. Added s_coxph_pairwise function perform pairwise testing, used t_tte t_coxph. Added methods t_count_true replacing t_summary_true. Updated t_count_unique create analysis subsets, added t_el_count_unique vectors. Fixed bug t_events_term_id table sort order decreasing frequency instead alphabetical. Added function color_palette new nest color palette.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-064","dir":"Changelog","previous_headings":"","what":"tern 0.6.4","title":"tern 0.6.4","text":"Refactored renaming functions utils.nest. Added event_type argument t_events_per_term_grade_id. Added one/two-arm t-test functions. Improvements t_summary_by. Internal code refactoring.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-063","dir":"Changelog","previous_headings":"","what":"tern 0.6.3","title":"tern 0.6.3","text":"related tree functions see reference trees. Moved label functions rtables. Deleted keys keys<- functions. Exported tabulate_pairwise. get_N, col_N_add_total, check_id. na_as_level. as_factor_keep_attributes. r_by. Disposition elementary table t_el_disposition. t_el_forest_tte, t_el_forest_rsp. Added table_tree argument returns node object. Added f_numeric choose statistics calculate. denominator now also allows omit wanting omit percentages. Renamed row_by. Changed functionality group_data using row_by_list. Removed na_omit_group. Removed indent argument, use indent function rtables. instead","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-062","dir":"Changelog","previous_headings":"","what":"tern 0.6.2","title":"tern 0.6.2","text":"Use cached data random.cdisc.data speed testing. Added t_summary.Date method. Added save_join.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-061","dir":"Changelog","previous_headings":"","what":"tern 0.6.1","title":"tern 0.6.1","text":"Fixed colors Kaplan-Meier Plot Changed width_row.names argument g_forest function width_row_names. Changed censor.show argument g_km function censor_show. Changed col.legend.title argument g_waterfall function col_legend_title. Changed na.rm argument t_count_unique function na_rm. Changed row.name argument t_count_unique function row_name. Changed na.omit.group argument t_forest_rsp function na_omit_group. Changed na.omit.group argument t_forest_tte function na_omit_group. Changed row.name.TRUE row.name.FALSE arguments t_summary.logical row_name_true row_name_false respectively. Rename splotTextGrob split_text_grob. Fix examples. Refactor internal functions code.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-060","dir":"Changelog","previous_headings":"","what":"tern 0.6.0","title":"tern 0.6.0","text":"Removed functions addTable, t_summarize_by_visit, t_summarize_variables. Added t_summary_by function. Refactor g_km function, renamed kmGrob kmCurveGrob. Refactor t_events_* family functions. Updated examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-tlgs-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New TLGs","title":"tern 0.5.0.3","text":"t_summary methods data.frame, numeric, logical, character, factor, Date objects. t_events_per_term_id, t_events_per_term_grade_id: Adverse Events & Concomitant Treatment Tables. t_max_grade_per_id, t_count_unique, t_events_summary elementary tables used Adverse Events & Concomitant Treatment Tables. g_waterfall: Horizontal Waterfall Plot.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"new-helper-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New Helper Functions","title":"tern 0.5.0.3","text":"decorate_grob, decorate_grob_set, decorate_grob_factory, splitTextGrob. stack_grobs, arrange_grobs, draw_grob.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tlg-changes-0-5-0-3","dir":"Changelog","previous_headings":"","what":"TLG changes","title":"tern 0.5.0.3","text":"t_tte now shows two rows ranges event censored times, respectively. g_km works one arm survfit objects. forest plot functions, added formatting display extreme values “>999.9”. t_summarise_variables uses now n instead N denominator calculating percentages factors default. t_rsp now works response values TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"deprecated-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"Deprecated Functions","title":"tern 0.5.0.3","text":"Deprecated t_summarize_variables t_summary powerful. Replacing t_summarize_by_visit t_summary_by occur upcoming release.","code":""},{"path":"https://insightsengineering.github.io/tern/main/news/index.html","id":"tern-050","dir":"Changelog","previous_headings":"","what":"tern 0.5.0","title":"tern 0.5.0","text":"First version harmonized analysis functions names arguments.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/tern/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/tern/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/tern/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"variable-class-conversion","dir":"Articles","previous_headings":"","what":"Variable Class Conversion","title":"Missing Values in Tern","text":"rtables requires split variables factors. try split variable isn’t, warning message appear. purposefully convert SEX variable character demonstrate happens try splitting rows variable. fix , df_explict_na convert factor resulting table generated.","code":"adsl <- tern_ex_adsl adsl$SEX <- as.character(adsl$SEX)  vars <- c(\"AGE\", \"SEX\", \"RACE\", \"BMRKR1\") var_labels <- c(   \"Age (yr)\",   \"Sex\",   \"Race\",   \"Continous Level Biomarker 1\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures #> Warning in as_factor_keep_attributes(x, verbose = verbose): automatically #> converting character variable x to factor, better manually convert to factor to #> avoid failures result #>                                                A: Drug X    B: Placebo    C: Combination   All Patients #>                                                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                                                #>   n                                               69            73              58             200      #>   Mean (SD)                                   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median                                         32.8          35.4            36.2            34.8     #>   Min - Max                                   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                                                     #>   n                                               69            73              58             200      #>   F                                           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                                           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)   #> Race                                                                                                    #>   n                                               69            73              58             200      #>   ASIAN                                       38 (55.1%)    43 (58.9%)       29 (50%)       110 (55%)   #>   BLACK OR AFRICAN AMERICAN                   15 (21.7%)    13 (17.8%)      12 (20.7%)       40 (20%)   #>   WHITE                                       11 (15.9%)    12 (16.4%)       11 (19%)        34 (17%)   #>   AMERICAN INDIAN OR ALASKA NATIVE             4 (5.8%)      3 (4.1%)       6 (10.3%)       13 (6.5%)   #>   MULTIPLE                                     1 (1.4%)      1 (1.4%)           0             2 (1%)    #>   NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0         1 (1.4%)           0            1 (0.5%)   #>   OTHER                                            0             0              0               0       #>   UNKNOWN                                          0             0              0               0       #> Continous Level Biomarker 1                                                                             #>   n                                               69            73              58             200      #>   Mean (SD)                                    6.3 (3.6)     6.7 (3.5)      6.2 (3.3)       6.4 (3.5)   #>   Median                                          5.4           6.3            5.4             5.6      #>   Min - Max                                   0.4 - 17.8    1.0 - 18.5      2.4 - 19.1      0.4 - 19.1"},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"including-missing-values-in-rtables","dir":"Articles","previous_headings":"","what":"Including Missing Values in rtables","title":"Missing Values in Tern","text":"purposefully convert M values NA SEX variable. running df_explicit_na NA values encoded <Missing> included table. well, missing values included n count included denominator value calculating percent values. want Na values displayed table included n count denominator calculating percent values, use na_level argument.","code":"adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               69            73              58             200      #>   Mean (SD)   34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median         32.8          35.4            36.2            34.8     #>   Min - Max   22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                     #>   n               38            40              32             110      #>   F            38 (100%)     40 (100%)      32 (100%)       110 (100%)  #>   M                0             0              0               0 adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                     A: Drug X    B: Placebo    C: Combination   All Patients #>                      (N=69)        (N=73)          (N=58)         (N=200)    #> ———————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                     #>   n                    69            73              58             200      #>   Mean (SD)        34.1 (6.8)    35.8 (7.1)      36.1 (7.4)      35.3 (7.1)  #>   Median              32.8          35.4            36.2            34.8     #>   Min - Max        22.4 - 48.0   23.3 - 57.5    23.0 - 58.3     22.4 - 58.3  #> Sex                                                                          #>   n                    69            73              58             200      #>   F                38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M                     0             0              0               0       #>   Missing Values   31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/articles/missing_values.html","id":"missing-values-in-numeric-variables","dir":"Articles","previous_headings":"","what":"Missing Values in Numeric Variables","title":"Missing Values in Tern","text":"Numeric variables missing values altered. means NA value numeric variable included summary statistics, included denominator value calculating percent values. make value less 30 missing AGE variable valued greater 30 included table .","code":"adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)  vars <- c(\"AGE\", \"SEX\") var_labels <- c(   \"Age (yr)\",   \"Sex\" )  result <- basic_table(show_colcounts = TRUE) %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) result #>                A: Drug X    B: Placebo    C: Combination   All Patients #>                 (N=69)        (N=73)          (N=58)         (N=200)    #> ——————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                #>   n               46            56              44             146      #>   Mean (SD)   37.8 (5.2)    38.3 (6.3)      39.1 (5.9)      38.3 (5.8)  #>   Median         37.2          37.3            37.5            37.5     #>   Min - Max   30.3 - 48.0   30.0 - 57.5    30.5 - 58.3     30.0 - 58.3  #> Sex                                                                     #>   n               69            73              58             200      #>   F           38 (55.1%)    40 (54.8%)      32 (55.2%)      110 (55%)   #>   M           31 (44.9%)    33 (45.2%)      26 (44.8%)       90 (45%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tern-tabulation","dir":"Articles","previous_headings":"","what":"tern Tabulation","title":"Tabulation","text":"tern R package provides functions create common analyses clinical trials R. core functionality tabulation built general purpose rtables package. New users first begin reading “Introduction tern” “Introduction rtables” vignettes. packages used vignette : datasets used vignette :","code":"library(rtables) library(tern) library(dplyr) adsl <- ex_adsl adae <- ex_adae adrs <- ex_adrs"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tern-analyze-functions","dir":"Articles","previous_headings":"","what":"tern Analyze Functions","title":"Tabulation","text":"Analyze functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analyze functions wrappers around rtables::analyze function, offer various methods useful perspective clinical trials statistical projects. Examples tern analyze functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analyze functions recommended use tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"internals-of-tern-analyze-functions","dir":"Articles","previous_headings":"tern Analyze Functions","what":"Internals of tern Analyze Functions","title":"Tabulation","text":"Please skip subsection interested internals tern analyze functions. Internally tern analyze functions like summarize_ancova mainly built 4 elements chain: descriptions function type: analysis helper functions h_*. functions useful help define analysis. statistics function s_*. Statistics functions computation numbers tabulated later. order separate computation formatting, take care rcell type formatting . formatted analysis functions a_*. arguments corresponding statistics functions, can customized calling rtables::make_afun() . used afun rtables::analyze(). analyze functions rtables::analyze(..., afun = make_afun(tern::a_*)). Analyze functions used combination rtables layout functions, pipeline creates table. last element chain. use native rtables::analyze function tern formatted analysis functions afun parameter. rtables::make_afun function helpful somebody wants attach format formatted analysis function.","code":"h_ancova() -> tern:::s_ancova() -> tern:::a_ancova() -> summarize_ancova() l <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = a_summary)  build_table(l, df = adrs) afun <- make_afun(     a_summary,     .stats = NULL,     .formats = c(median = \"xx.\"),     .labels = c(median = \"My median\"),     .indent_mods = c(median = 1L) )  l2 <- basic_table() %>%     split_cols_by(var = \"ARM\") %>%     split_rows_by(var = \"AVISIT\") %>%     analyze(vars = \"AVAL\", afun = afun)  build_table(l2, df = adrs)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"tabulation-examples","dir":"Articles","previous_headings":"","what":"Tabulation Examples","title":"Tabulation","text":"going create 3 different tables using tern analyze functions rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"demographic-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Demographic Table","title":"Tabulation","text":"Demographic tables provide summary characteristics patients enrolled clinical trial. Typically table columns represent treatment arms variables summarized table demographic properties age, sex, race, etc. example function tern analyze_vars() remaining layout functions rtables. change display order categorical variables table use factor variables explicitly set order levels. case display order columns rows. Note forcats package many useful functions help types data processing steps (used ). tern package includes many functions similar analyze_vars(). functions called layout creating functions used combination rtables layout functions just like examples . Layout creating functions wrapping calls rtables analyze(), analyze_colvars() summarize_row_groups() provide options easy formatting analysis modifications. customize display demographics table, can via arguments analyze_vars(). layout creating functions tern include standard arguments .stats, .formats, .labels .indent_mods control statistics displayed numbers formatted. Refer package help help(\"analyze_vars\") ?analyze_vars see full set options. example change default summary numeric variables include number records, mean standard deviation (single statistic, .e. within single cell). categorical variables modify summary include number records counts categories. also modify display format mean standard deviation print two decimal places instead just one. One feature layout can used different datasets create different summaries. example, can easily create summary demographics Brazil China subgroups, respectively:","code":"# Select variables to include in table. vars <- c(\"AGE\", \"SEX\") var_labels <- c(\"Age (yr)\", \"Sex\")  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                       A: Drug X    B: Placebo    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          33.8 (6.6)    35.4 (7.9)      35.4 (7.7)      34.9 (7.4)  #>   Median                33.0          35.0            35.0            34.0     #>   Min - Max          21.0 - 50.0   21.0 - 62.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   F                   79 (59%)     77 (57.5%)       66 (50%)      222 (55.5%)  #>   M                  51 (38.1%)     55 (41%)       60 (45.5%)     166 (41.5%)  #>   U                   3 (2.2%)      2 (1.5%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED    1 (0.7%)          0           2 (1.5%)        3 (0.8%) # Reorder the levels in the ARM variable. adsl$ARM <- factor(adsl$ARM, levels = c(\"B: Placebo\", \"A: Drug X\", \"C: Combination\"))  # Reorder the levels in the SEX variable. adsl$SEX <- factor(adsl$SEX, levels = c(\"M\", \"F\", \"U\", \"UNDIFFERENTIATED\"))  basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   ) %>%   build_table(adsl) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=134)       (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      134           134            132             400      #>   Mean (SD)          35.4 (7.9)    33.8 (6.6)      35.4 (7.7)      34.9 (7.4)  #>   Median                35.0          33.0            35.0            34.0     #>   Min - Max          21.0 - 62.0   21.0 - 50.0    20.0 - 69.0     20.0 - 69.0  #> Sex                                                                            #>   n                      134           134            132             400      #>   M                   55 (41%)     51 (38.1%)      60 (45.5%)     166 (41.5%)  #>   F                  77 (57.5%)     79 (59%)        66 (50%)      222 (55.5%)  #>   U                   2 (1.5%)      3 (2.2%)         4 (3%)         9 (2.2%)   #>   UNDIFFERENTIATED        0         1 (0.7%)        2 (1.5%)        3 (0.8%) # Select statistics and modify default formats. basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels,     .stats = c(\"n\", \"mean_sd\", \"count\"),     .formats = c(mean_sd = \"xx.xx (xx.xx)\")   ) %>%   build_table(adsl) #>                       B: Placebo     A: Drug X     C: Combination   All Patients #>                        (N=134)        (N=134)         (N=132)         (N=400)    #> ———————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                         #>   n                      134            134             132             400      #>   Mean (SD)          35.43 (7.90)   33.77 (6.55)    35.43 (7.72)    34.88 (7.44) #> Sex                                                                              #>   n                      134            134             132             400      #>   M                       55             51              60             166      #>   F                       77             79              66             222      #>   U                       2              3               4               9       #>   UNDIFFERENTIATED        0              1               2               3 lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_overall_col(\"All Patients\") %>%   add_colcounts() %>%   analyze_vars(     vars = vars,     var_labels = var_labels   )  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"BRA\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                         (N=7)        (N=13)          (N=10)          (N=30)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                       7            13              10              30      #>   Mean (SD)          32.0 (6.1)    36.7 (6.4)     38.3 (10.6)      36.1 (8.1)  #>   Median                32.0          37.0            35.0            35.5     #>   Min - Max          25.0 - 42.0   24.0 - 47.0    25.0 - 64.0     24.0 - 64.0  #> Sex                                                                            #>   n                       7            13              10              30      #>   M                   4 (57.1%)     8 (61.5%)       5 (50%)        17 (56.7%)  #>   F                   3 (42.9%)     5 (38.5%)       5 (50%)        13 (43.3%)  #>   U                       0             0              0               0       #>   UNDIFFERENTIATED        0             0              0               0  build_table(lyt, df = adsl %>% dplyr::filter(COUNTRY == \"CHN\")) #>                      B: Placebo     A: Drug X    C: Combination   All Patients #>                        (N=81)        (N=74)          (N=64)         (N=219)    #> —————————————————————————————————————————————————————————————————————————————— #> Age (yr)                                                                       #>   n                      81            74              64             219      #>   Mean (SD)          35.7 (7.3)    33.0 (6.4)      35.2 (6.4)      34.6 (6.8)  #>   Median                36.0          32.0            35.0            34.0     #>   Min - Max          21.0 - 58.0   23.0 - 48.0    21.0 - 49.0     21.0 - 58.0  #> Sex                                                                            #>   n                      81            74              64             219      #>   M                  35 (43.2%)    27 (36.5%)      30 (46.9%)       92 (42%)   #>   F                  45 (55.6%)    44 (59.5%)      29 (45.3%)     118 (53.9%)  #>   U                   1 (1.2%)      2 (2.7%)        3 (4.7%)        6 (2.7%)   #>   UNDIFFERENTIATED        0         1 (1.4%)        2 (3.1%)        3 (1.4%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"adverse-event-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Adverse Event Table","title":"Tabulation","text":"standard table adverse events summary system organ class preferred term. frequency counts preferred term, multiple occurrences AE individual count . create table need use combination several layout creating functions tabulation pipeline. start creating high-level summary. layout creating function tern can summarize_num_patients(): Note table, denominator used percentages shown header table (N = xx) defined based subject-level dataset adsl. done using alt_df_counts argument build_table(), provides alternative data set deriving counts header. often required work data sets include multiple records per patient df, adae .","code":"basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                  A: Drug X    B: Placebo    C: Combination   All Patients #>                                                   (N=134)       (N=134)        (N=132)         (N=400)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE   122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                      609           622            703             1934"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"statistics-functions","dir":"Articles","previous_headings":"Tabulation Examples > Adverse Event Table","what":"Statistics Functions","title":"Tabulation","text":"building rest AE table helpful introduce tern package design conventions. layout creating function tern wrapper Statistics function. Statistics functions ones actual computation numbers table. functions always return named lists whose elements statistics available include layout via .stats argument layout creating function level. Statistics functions follow naming convention always begin s_* ease use documented page layout creating function counterpart. helpful review Statistic function understand logic used calculate numbers table see options may available modify analysis. example, Statistics function calculating numbers summarize_num_patients() s_num_patients(). results Statistics function list elements unique, nonunique unique_count: results can see unique nonunique statistics displayed “Patients” column initial AE table output . Also can see raw numbers formatted way. formatting functionality handled layout creating function level .formats argument. Now know types statistics can derived s_num_patients(), can try modifying default layout returned summarize_num_patients(). Instead reporting unique nonqunie statistics, specify analysis include unique_count statistic. result show counts unique patients. Note make update .stats .labels argument summarize_num_patients(). Let’s now continue building layout adverse event table. top-level summary, can repeat summary system organ class level. split analysis data split_rows_by() calling summarize_num_patients(). table looks almost ready. final step, need layout creating function can produce count table event frequencies. layout creating function count_occurrences(). Let’s first try using function simpler layout without row splits: Putting everything together, final AE table looks like :","code":"s_num_patients(x = adae$USUBJID, labelstr = \"\", .N_col = nrow(adae)) #> $unique #> [1] 365.000000   0.188728 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 1934 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 365 #> attr(,\"label\") #> [1] \"(n)\" basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\",     .labels = c(unique_count = \"Total number of patients with at least one AE\")   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                 A: Drug X   B: Placebo   C: Combination   All Patients #>                                                  (N=134)     (N=134)        (N=132)         (N=400)    #> —————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE      122         123            120             365 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208 basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                 A: Drug X    B: Placebo   C: Combination   All Patients #>                  (N=134)      (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————— #> dcd A.1.1.1.1   50 (37.3%)   45 (33.6%)     63 (47.7%)     158 (39.5%)  #> dcd A.1.1.1.2   48 (35.8%)   48 (35.8%)     50 (37.9%)     146 (36.5%)  #> dcd B.1.1.1.1   47 (35.1%)   49 (36.6%)     43 (32.6%)     139 (34.8%)  #> dcd B.2.1.2.1   49 (36.6%)   44 (32.8%)     52 (39.4%)     145 (36.2%)  #> dcd B.2.2.3.1   48 (35.8%)   54 (40.3%)     51 (38.6%)     153 (38.2%)  #> dcd C.1.1.1.3   43 (32.1%)   46 (34.3%)     43 (32.6%)     132 (33.0%)  #> dcd C.2.1.2.1   35 (26.1%)   48 (35.8%)     55 (41.7%)     138 (34.5%)  #> dcd D.1.1.1.1   50 (37.3%)   42 (31.3%)     51 (38.6%)     143 (35.8%)  #> dcd D.1.1.4.2   48 (35.8%)   42 (31.3%)     50 (37.9%)     140 (35.0%)  #> dcd D.2.1.5.3   47 (35.1%)   58 (43.3%)     57 (43.2%)     162 (40.5%) basic_table() %>%   split_cols_by(var = \"ACTARM\") %>%   add_colcounts() %>%   add_overall_col(label = \"All Patients\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   split_rows_by(     \"AEBODSYS\",     child_labels = \"visible\",     nested = FALSE,     indent_mod = -1L,     split_fun = drop_split_levels   ) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       unique = \"Total number of patients with at least one AE\",       nonunique = \"Overall total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\") %>%   build_table(     df = adae,     alt_counts_df = adsl   ) #>                                                    A: Drug X    B: Placebo    C: Combination   All Patients #>                                                     (N=134)       (N=134)        (N=132)         (N=400)    #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one AE     122 (91.0%)   123 (91.8%)    120 (90.9%)     365 (91.2%)  #> Overall total number of events                        609           622            703             1934     #> cl A.1                                                                                                      #>   Total number of patients with at least one AE   78 (58.2%)    75 (56.0%)      89 (67.4%)     242 (60.5%)  #>   Overall total number of events                      132           130            160             422      #>     dcd A.1.1.1.1                                 50 (37.3%)    45 (33.6%)      63 (47.7%)     158 (39.5%)  #>     dcd A.1.1.1.2                                 48 (35.8%)    48 (35.8%)      50 (37.9%)     146 (36.5%)  #> cl B.1                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #>   Overall total number of events                      56            60              62             178      #>     dcd B.1.1.1.1                                 47 (35.1%)    49 (36.6%)      43 (32.6%)     139 (34.8%)  #> cl B.2                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    74 (55.2%)      85 (64.4%)     238 (59.5%)  #>   Overall total number of events                      129           138            143             410      #>     dcd B.2.1.2.1                                 49 (36.6%)    44 (32.8%)      52 (39.4%)     145 (36.2%)  #>     dcd B.2.2.3.1                                 48 (35.8%)    54 (40.3%)      51 (38.6%)     153 (38.2%)  #> cl C.1                                                                                                      #>   Total number of patients with at least one AE   43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #>   Overall total number of events                      55            63              64             182      #>     dcd C.1.1.1.3                                 43 (32.1%)    46 (34.3%)      43 (32.6%)     132 (33.0%)  #> cl C.2                                                                                                      #>   Total number of patients with at least one AE   35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #>   Overall total number of events                      48            53              65             166      #>     dcd C.2.1.2.1                                 35 (26.1%)    48 (35.8%)      55 (41.7%)     138 (34.5%)  #> cl D.1                                                                                                      #>   Total number of patients with at least one AE   79 (59.0%)    67 (50.0%)      80 (60.6%)     226 (56.5%)  #>   Overall total number of events                      127           106            135             368      #>     dcd D.1.1.1.1                                 50 (37.3%)    42 (31.3%)      51 (38.6%)     143 (35.8%)  #>     dcd D.1.1.4.2                                 48 (35.8%)    42 (31.3%)      50 (37.9%)     140 (35.0%)  #> cl D.2                                                                                                      #>   Total number of patients with at least one AE   47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)  #>   Overall total number of events                      62            72              74             208      #>     dcd D.2.1.5.3                                 47 (35.1%)    58 (43.3%)      57 (43.2%)     162 (40.5%)"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"response-table","dir":"Articles","previous_headings":"Tabulation Examples","what":"Response Table","title":"Tabulation","text":"typical response table binary clinical trial endpoint may composed several different analyses: Proportion responders treatment group Difference proportion responders comparison groups vs. control group Chi-Square test difference response rates comparison groups vs. control group can build table layout like following approach used AE table: table section produced using different layout creating function tern. First start data preparation steps set analysis dataset. select endpoint analyze PARAMCD define logical variable is_rsp indicates whether patient classified responder . create summary proportion responders treatment group, use estimate_proportion() layout creating function: specify arm table used reference, use argument ref_group split_cols_by(). change reference arm “B: Placebo” arm displayed first column: customize analysis, can use method conf_level arguments modify type confidence interval calculated: next table section needed summarize difference response rates reference arm comparison arm. Use estimate_proportion_diff() layout creating function : final section needed complete table includes statistical test difference response rates. Use test_proportion_diff() layout creating function : customize output, use method argument select Chi-Squared test Schouten correction. Now can put table sections together one layout pipeline. Note one small change needed. Since primary analysis variable table sections (is_rsp), need give sub-table unique name. done adding table_names argument providing unique names :","code":"# Preprocessing to select an analysis endpoint. anl <- adrs %>%   dplyr::filter(PARAMCD == \"BESRSPI\") %>%   dplyr::mutate(is_rsp = AVALC %in% c(\"CR\", \"PR\")) basic_table() %>%   split_cols_by(var = \"ARM\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     table_names = \"est_prop\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\"   ) %>%   build_table(anl) #>                                   A: Drug X      B: Placebo    C: Combination #>                                    (N=134)        (N=134)         (N=132)     #> ————————————————————————————————————————————————————————————————————————————— #> Responders                       114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 95% CI (Wald, with correction)   (78.7, 91.5)   (58.8, 75.5)    (85.6, 96.2) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9   ) %>%   build_table(anl) #>                             A: Drug X      B: Placebo    C: Combination #>                              (N=134)        (N=134)         (N=132)     #> ——————————————————————————————————————————————————————————————————————— #> Responders                 114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)   (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(anl) #>                                       A: Drug X    B: Placebo   C: Combination #>                                        (N=134)      (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————————————— #> Unstratified Analysis                                                          #>   Difference in Response rate (%)       17.9                         23.7      #>     95% CI (Wald, with correction)   (7.2, 28.6)                 (13.7, 33.8) basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(vars = \"is_rsp\") %>%   build_table(anl) #>                                A: Drug X   B: Placebo   C: Combination #>                                 (N=134)     (N=134)        (N=132)     #> —————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test)    0.0006                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\"   ) %>%   build_table(anl) #>                                                         A: Drug X   B: Placebo   C: Combination #>                                                          (N=134)     (N=134)        (N=132)     #> ——————————————————————————————————————————————————————————————————————————————————————————————— #>   p-value (Chi-Squared Test with Schouten Correction)    0.0008                     <0.0001 basic_table() %>%   split_cols_by(var = \"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   estimate_proportion(     vars = \"is_rsp\",     method = \"clopper-pearson\",     conf_level = 0.9,     table_names = \"est_prop\"   ) %>%   estimate_proportion_diff(     vars = \"is_rsp\",     show_labels = \"visible\",     var_labels = \"Unstratified Analysis\",     table_names = \"est_prop_diff\"   ) %>%   test_proportion_diff(     vars = \"is_rsp\",     method = \"schouten\",     table_names = \"test_prop_diff\"   ) %>%   build_table(anl) #>                                                          A: Drug X      B: Placebo    C: Combination #>                                                           (N=134)        (N=134)         (N=132)     #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> Responders                                              114 (85.1%)     90 (67.2%)     120 (90.9%)   #> 90% CI (Clopper-Pearson)                                (79.1, 89.9)   (59.9, 73.9)    (85.7, 94.7)  #> Unstratified Analysis                                                                                #>   Difference in Response rate (%)                           17.9                           23.7      #>     95% CI (Wald, with correction)                      (7.2, 28.6)                    (13.7, 33.8)  #>   p-value (Chi-Squared Test with Schouten Correction)      0.0008                        <0.0001"},{"path":"https://insightsengineering.github.io/tern/articles/tables.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Tabulation","text":"Tabulation tern builds top layout tabulation framework rtables. Complex tables built step step pipeline combining layout creating functions perform specific type analysis. tern analyze functions introduced vignette : analyze_vars() summarize_num_patients() count_occurrences() estimate_proportion() estimate_proportion_diff() test_proportion_diff() Layout creating functions build formatted layout controlling features labels, numerical display formats indentation. functions wrappers Statistics functions calculate raw summaries analysis. can easily spot Statistics functions documentation always begin prefix s_. can helpful inspect run Statistics functions understand ways analysis can customized.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"common-clinical-trials-analyses","dir":"Articles","previous_headings":"","what":"Common Clinical Trials Analyses","title":"Introduction to tern","text":"package provides large range functionality create tables graphs used clinical trial statistical analysis. rtables tabulation extended clinical trials specific functions: demographics unique patients exposure across patients change baseline parameters statistical model fits: MMRM, logistic regression, Cox regression, … … rtables tabulation helper functions: pre-processing conversions transformations … data visualizations connected clinical trials: Kaplan-Meier plots forest plots line plots … data visualizations helper functions: arrange/stack multiple graphs embellishing graphs/tables metadata details, adding titles, footnotes, page number, etc. … reference tern functions available tern website functions reference.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"analytical-functions-for-rtables","dir":"Articles","previous_headings":"","what":"Analytical Functions for rtables","title":"Introduction to tern","text":"Analytical functions used combination rtables layout functions, pipeline creates rtables table. apply statistical logic layout rtables table. table layout materialized rtables::build_table function data. tern analytical functions wrappers around rtables::analyze function; offer various methods useful perspective clinical trials statistical projects. Examples tern analytical functions count_occurrences, summarize_ancova analyze_vars. one prefix identify tern analytical functions recommended use reference subsection tern website. rtables code first describe two tables assign descriptions variables lyt lyt2. built tables using actual data rtables::build_table. description table called table layout. analyze instruction adds layout ARM variable analyzed mean analysis function result rounded 1 decimal place. Hence, layout “pre-data”; , ’s description build table get data. Defining table layout pure rtables code: , tern function used analyze_vars replaces rtables::analyze function used . see tern offers advanced analysis extending rtables function calls one additional function call. examples tabulation analyze functions presented Tabulation vignette.","code":"library(tern) library(dplyr) # Create table layout pure rtables lyt <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   rtables::analyze(vars = \"AVAL\", mean, format = \"xx.x\") # Create table layout with tern analyze_vars analyze function lyt2 <- rtables::basic_table() %>%   rtables::split_cols_by(var = \"ARM\") %>%   rtables::split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", .formats = c(\"mean_sd\" = \"(xx.xx, xx.xx)\")) # Apply table layout to data and produce `rtables` object  adrs <- formatters::ex_adrs  rtables::build_table(lyt, df = adrs) #>                    A: Drug X   B: Placebo   C: Combination #> —————————————————————————————————————————————————————————— #> SCREENING                                                  #>   mean                3.0         3.0            3.0       #> BASELINE                                                   #>   mean                2.5         2.8            2.5       #> END OF INDUCTION                                           #>   mean                1.7         2.1            1.6       #> FOLLOW UP                                                  #>   mean                2.2         2.9            2.0 rtables::build_table(lyt2, df = adrs) #>                     A: Drug X      B: Placebo    C: Combination #> ——————————————————————————————————————————————————————————————— #> SCREENING                                                       #>   n                    154            178             144       #>   Mean (SD)        (3.00, 0.00)   (3.00, 0.00)    (3.00, 0.00)  #>   Median               3.0            3.0             3.0       #>   Min - Max         3.0 - 3.0      3.0 - 3.0       3.0 - 3.0    #> BASELINE                                                        #>   n                    136            146             124       #>   Mean (SD)        (2.46, 0.88)   (2.77, 1.00)    (2.46, 1.08)  #>   Median               3.0            3.0             3.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> END OF INDUCTION                                                #>   n                    218            205             217       #>   Mean (SD)        (1.75, 0.90)   (2.14, 1.28)    (1.65, 1.06)  #>   Median               2.0            2.0             1.0       #>   Min - Max         1.0 - 4.0      1.0 - 5.0       1.0 - 5.0    #> FOLLOW UP                                                       #>   n                    164            153             167       #>   Mean (SD)        (2.23, 1.26)   (2.89, 1.29)    (1.97, 1.01)  #>   Median               2.0            4.0             2.0       #>   Min - Max         1.0 - 4.0      1.0 - 4.0       1.0 - 4.0"},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"clinical-trial-visualizations","dir":"Articles","previous_headings":"","what":"Clinical Trial Visualizations","title":"Introduction to tern","text":"Clinical trial related plots complement rich palette tern tabulation analysis functions. Thus tern package delivers full-featured tool clinical trial reporting. tern plot functions return graphs ggplot2 objects. optional nestcolor package can loaded apply standardized NEST color palette tern plots. Line plot without table generated g_lineplot function.  Line plot table generated g_lineplot function.  tern functions used plot generation g_ prefixed listed tern website functions reference.","code":"adsl <- formatters::ex_adsl adlb <- formatters::ex_adlb adlb <- dplyr::filter(adlb, PARAMCD == \"ALT\", AVISIT != \"SCREENING\") library(nestcolor) # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\") # Mean with CI, table, and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )"},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"interactive-apps","dir":"Articles","previous_headings":"","what":"Interactive Apps","title":"Introduction to tern","text":"tern outputs can easily converted shiny apps. recommend building apps using teal package, shiny-based interactive exploration framework analyzing data. variety pre-made teal shiny apps tern outputs available teal.modules.clinical package.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Introduction to tern","text":"summary, tern contains many additional functions creating tables, listings, graphs used clinical trials statistical analyses. design package gives users flexibility meet analysis needs regulatory exploratory reporting contexts. information please explore tern website.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"tern-formatting-functions-overview","dir":"Articles","previous_headings":"","what":"tern Formatting Functions Overview","title":"Formatting Functions","text":"tern R package provides functions create common analyses clinical trials R functions default formatting arguments displaying values output specific way. tern formatting differs compared formatting available formatters package tern formats capable handling logical statements, allowing fine-tuning output displayed. Depending type value displayed, value , format output change. Whereas using formatters package, specified format applied regardless value. see available formatting functions available tern see ?formatting_functions. see available format strings available formatters see formatters::list_valid_format_labels().","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"comparing-tern-formatters-formats","dir":"Articles","previous_headings":"","what":"Comparing tern & formatters Formats","title":"Formatting Functions","text":"packages used vignette : example demonstrates use tern formatting count_abnormal() function. example “low” category non-zero numerator value fraction percentage value displayed, “high” value numerator value zero fraction value displayed without also displaying redundant zero percentage value. following example count_abnormal() function utilized . time “low” values “high” values non-zero numerator show percentage. following example demonstrates difference formatters used instead format output. choose use \"xx / xx\" value format. “high” value zero numerator value “low” value non-zero numerator, yet displayed format. concept occurs using available formats formatters package. following example displays result using \"xx.x / xx.x\" format instead. Use formatters::list_valid_format_labels() see full list available formats formatters.","code":"library(rtables) library(formatters) library(tern) library(dplyr) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs   #> ————————————————— #> low    2/2 (100%) #> high      0/2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction)   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%) df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx / xx\")   ) %>%   build_table(df2) #>        all obs #> —————————————— #> low     2 / 2  #> high    0 / 2 df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = \"xx.x / xx.x\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    2.0 / 2.0 #> high   0.0 / 2.0"},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"formatting-function-basics","dir":"Articles","previous_headings":"","what":"Formatting Function Basics","title":"Formatting Functions","text":"Current tern formatting functions consider following aspects setting custom behaviors: Missing values - custom value string can set display missing values instead NA. 0’s - cell value zero, tern fraction formatting functions exclude accompanying percentage value. Number decimal places display - number decimal places can fixed needed. Value thresholds - different format value can displayed depending whether value within certain threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"number-of-decimal-places-to-display","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Number of Decimal Places to Display","title":"Formatting Functions","text":"Two functions set fixed number decimal places (specifically 1) format_fraction_fixed_dp() format_count_fraction_fixed_dp(). default, formatting functions remove trailing zeros, two functions always one decimal place percentage, even digit zero. See following example:","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 3L)) #> [1] \"1/3 (33.3%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\"  format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.25)) #> [1] \"2 (25.0%)\""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"value-thresholds","dir":"Articles","previous_headings":"Formatting Function Basics","what":"Value Thresholds","title":"Formatting Functions","text":"Functions set custom values according certain threshold include format_extreme_values(), format_extreme_values_ci(), format_fraction_threshold(). extreme value formats work similarly allow user specify maximum number digits include, large small values given special string value. example: format_fraction_threshold() function allows user specify lower percentage threshold, values instead assigned special string value. example: See documentation function specific details behavior customize .","code":"extreme_format <- format_extreme_values(digits = 2) extreme_format(0.235) #> [1] \"0.23\" extreme_format(0.001) #> [1] \"<0.01\" extreme_format(Inf) #> [1] \">999.99\" fraction_format <- format_fraction_threshold(0.05) fraction_format(x = c(20, 0.1)) #> [1] 10 fraction_format(x = c(2, 0.01)) #> [1] \"<5\""},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"creating-custom-formatting-functions","dir":"Articles","previous_headings":"","what":"Creating Custom Formatting Functions","title":"Formatting Functions","text":"table requires customized output displayed using one pre-existing tern formatting functions, may want consider creating new formatting function. creating formatting function important consider aspects listed Formatting Function Customization section . section create custom formatting function derived format_fraction_fixed_dp() function. First take look function detail customize . see numerator value greater 0, fraction percentage displayed. numerator 0, fraction shown. Percent values always display 1 decimal place. create dummy dataset observe output value behavior formatting function applied. Now modify function make custom formatting function, custom_format. want display 3 decimal places percent value, numerator value 0 want display 0 value (without denominator).","code":"# First we will see how the format_fraction_fixed_dp code works and displays the outputs format_fraction_fixed_dp <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"], \"/\", x[\"denom\"])   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\"     )   }   return(result) } df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"LOW\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE ) %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = format_fraction_fixed_dp)   ) %>%   build_table(df2) #>          all obs    #> ——————————————————— #> low    2/2 (100.0%) #> high       0/2 custom_format <- function(x, ...) {   attr(x, \"label\") <- NULL   checkmate::assert_vector(x)   checkmate::assert_count(x[\"num\"])   checkmate::assert_count(x[\"denom\"])    result <- if (x[\"num\"] == 0) {     paste0(x[\"num\"]) # We remove the denominator on this line so that only a 0 is displayed   } else {     paste0(       x[\"num\"], \"/\", x[\"denom\"],       \" (\", sprintf(\"%.3f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" # We include 3 decimal places with %.3f     )   }   return(result) }  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\"),     exclude_base_abn = FALSE,     .formats = list(fraction = custom_format) # Here we implement our new custom_format function   ) %>%   build_table(df2) #>           all obs     #> ————————————————————— #> low    2/2 (100.000%) #> high         0"},{"path":"https://insightsengineering.github.io/tern/articles/tern_formats.html","id":"summary","dir":"Articles","previous_headings":"","what":"Summary","title":"Formatting Functions","text":"tern analysis function pre-specified default format functions implement generating output, taken formatters package custom formatting functions stored tern. tern functions differ compared formatters logical statements can used set value-dependent customized formats. like create custom formatting function use tern, sure carefully consider rules want implement handle different input values.","code":""},{"path":"https://insightsengineering.github.io/tern/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Joe Zhu. Author, maintainer. Daniel Sabanés Bové. Author. Jana Stoilova. Author. Davide Garolini. Author. Emily de la Rua. Author. Abinaya Yogasekaram. Author. Heng Wang. Author. Francois Collin. Author. Adrian Waddell. Author. Pawel Rucki. Author. Chendi Liao. Author. Jennifer Li. Author. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/tern/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhu J, Sabanés Bové D, Stoilova J, Garolini D, de la Rua E, Yogasekaram , Wang H, Collin F, Waddell , Rucki P, Liao C, Li J (2024). tern: Create Common TLGs Used Clinical Trials. R package version 0.9.6.9006, https://github.com/insightsengineering/tern/, https://insightsengineering.github.io/tern/.","code":"@Manual{,   title = {tern: Create Common TLGs Used in Clinical Trials},   author = {Joe Zhu and Daniel {Sabanés Bové} and Jana Stoilova and Davide Garolini and Emily {de la Rua} and Abinaya Yogasekaram and Heng Wang and Francois Collin and Adrian Waddell and Pawel Rucki and Chendi Liao and Jennifer Li},   year = {2024},   note = {R package version 0.9.6.9006,     https://github.com/insightsengineering/tern/},   url = {https://insightsengineering.github.io/tern/}, }"},{"path":"https://insightsengineering.github.io/tern/index.html","id":"tern-","dir":"","previous_headings":"","what":"Create Common TLGs Used in Clinical Trials","title":"Create Common TLGs Used in Clinical Trials","text":"tern R package contains analysis functions create tables graphs used clinical trial reporting. package provides large range functionality, : Data visualizations: Line plots (g_lineplot) Kaplan-Meier plots (g_km) Forest plots (g_forest) STEP graphs (g_step) Individual patient plots (g_ipp) Waterfall plots (g_waterfall) Bland-Altman plots (g_bland_altman) Statistical model fit summaries: Logistic regression (summarize_logistic) Cox regression (summarize_coxreg) Analysis tables: See list available analyze functions See list available summarize functions See list available column-wise analysis functions Many outputs available added teal shiny applications interactive exploration data. teal modules available teal.modules.clinical package. See TLG Catalog extensive catalog example clinical trial tables, listings, graphs created using tern functionality.","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Create Common TLGs Used in Clinical Trials","text":"tern available CRAN can install latest released version : can install latest development version directly GitHub running following:","code":"install.packages(\"tern\") # install.packages(\"pak\") pak::pak(\"insightsengineering/tern\")"},{"path":"https://insightsengineering.github.io/tern/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Create Common TLGs Used in Clinical Trials","text":"understand use package, please refer Introduction tern article, provides multiple examples code implementation. See package vignettes browseVignettes(package = \"tern\") usage package.","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"related","dir":"","previous_headings":"","what":"Related","title":"Create Common TLGs Used in Clinical Trials","text":"rtables - table engine used tlg-catalog - website showcasing many examples clinical trial tables, listings, graphs teal.modules.clinical - teal modules interactive data analysis","code":""},{"path":"https://insightsengineering.github.io/tern/index.html","id":"acknowledgment","dir":"","previous_headings":"","what":"Acknowledgment","title":"Create Common TLGs Used in Clinical Trials","text":"package result joint efforts many developers stakeholders. like thank everyone contributed far!","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal range values — abnormal","title":"Count patients with abnormal range values — abnormal","text":"analyze function count_abnormal() creates layout element count patients abnormal analysis range values direction. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), fraction patient counts returned, numerator denominator calculated follows: num: number patients abnormality recorded treatment. denom: total number patients least one post-baseline assessment. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal range values — abnormal","text":"","code":"count_abnormal(   lyt,   var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )  a_count_abnormal(   df,   .var,   abnormal = list(Low = \"LOW\", High = \"HIGH\"),   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   exclude_base_abn = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal range values — abnormal","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (named list) list identifying abnormal range level(s) var. Defaults list(Low = \"LOW\", High = \"HIGH\") can also group different levels named list, example, abnormal = list(Low = c(\"LOW\", \"LOW LOW\"), High = c(\"HIGH\", \"HIGH HIGH\")). variables (named list string) list additional analysis variables. exclude_base_abn (flag) whether exclude subjects baseline abnormality numerator denominator. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal() table layout. s_count_abnormal() returns statistic fraction vector num denom counts patients. a_count_abnormal() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal(): Statistics function counts patients abnormal range values single abnormal level. a_count_abnormal(): Formatted analysis function used afun count_abnormal().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal range values — abnormal","text":"count_abnormal() considers single variable contains multiple abnormal levels. df filtered include post-baseline records. denominator includes patients may abnormal levels baseline, patients missing baseline records. Patients abnormalities baseline can optionally excluded numerator denominator via exclude_base_abn parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal range values — abnormal","text":"","code":"library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following object is masked from ‘package:testthat’: #>  #>     matches #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union  df <- data.frame(   USUBJID = as.character(c(1, 1, 2, 2)),   ANRIND = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BNRIND = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df <- df %>%   filter(ONTRTFL == \"Y\")  # Layout creating function. basic_table() %>%   count_abnormal(var = \"ANRIND\", abnormal = list(high = \"HIGH\", low = \"LOW\")) %>%   build_table(df) #>         all obs  #> ———————————————— #> high   1/2 (50%) #> low    1/2 (50%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 1, 2, 2)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BL_RANGE = factor(c(\"NORMAL\", \"NORMAL\", \"HIGH\", \"HIGH\")),   ONTRTFL = c(\"\", \"Y\", \"\", \"Y\"),   stringsAsFactors = FALSE )  # Select only post-baseline records. df2 <- df2 %>%   filter(ONTRTFL == \"Y\")  basic_table() %>%   count_abnormal(     var = \"RANGE\",     abnormal = list(low = \"LOW\", high = \"HIGH\"),     variables = list(id = \"ID\", baseline = \"BL_RANGE\")   ) %>%   build_table(df2) #>         all obs  #> ———————————————— #> low    1/2 (50%) #> high   1/2 (50%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"analyze function count_abnormal_by_baseline() creates layout element count patients abnormal analysis range values, categorized baseline status. function analyzes primary analysis variable var indicates abnormal range results. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline (defaults BNRIND), variable indicate baseline reference ranges. direction specified via abnormal parameter (e.g. High Low), condition baseline range result count patients numerator denominator follows following categories: <abnormality> num:  number patients without abnormality baseline (excluding missing baseline) least one abnormality post-baseline. denom: number patients without abnormality baseline (excluding missing baseline). <Abnormality> num: number patients abnormality baseline least one abnormality post-baseline. denom: number patients abnormality baseline. Total num: number patients least one post-baseline record least one abnormality post-baseline. denom: number patients least one post-baseline record. function assumes df filtered include post-baseline records.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"count_abnormal_by_baseline(   lyt,   var,   abnormal,   variables = list(id = \"USUBJID\", baseline = \"BNRIND\"),   na_str = \"<Missing>\",   nested = TRUE,   ...,   table_names = abnormal,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )  a_count_abnormal_by_baseline(   df,   .var,   abnormal,   na_str = \"<Missing>\",   variables = list(id = \"USUBJID\", baseline = \"BNRIND\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"lyt (PreDataTableLayouts) layout analyses added . abnormal (character) values identifying abnormal range level(s) .var. variables (named list string) list additional analysis variables. na_str (string) explicit na_level argument used pre-processing steps (maybe df_explicit_na()). default \"<Missing>\". nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_baseline() table layout. s_count_abnormal_by_baseline() returns statistic fraction named list 3 labeled elements: not_abnormal, abnormal, total. element contains vector num denom patient counts. a_count_abnormal_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"count_abnormal_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_baseline(): Statistics function single abnormal level. a_count_abnormal_by_baseline(): Formatted analysis function used afun count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"df filtered include post-baseline records. baseline variable analysis variable contains NA records, expected df pre-processed using df_explicit_na() explicit_na().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with abnormal analysis range values by baseline status — abnormal_by_baseline","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1:6)),   ANRIND = factor(c(rep(\"LOW\", 4), \"NORMAL\", \"HIGH\")),   BNRIND = factor(c(\"LOW\", \"NORMAL\", \"HIGH\", NA, \"LOW\", \"NORMAL\")) ) df <- df_explicit_na(df)  # Layout creating function. basic_table() %>%   count_abnormal_by_baseline(var = \"ANRIND\", abnormal = c(High = \"HIGH\")) %>%   build_table(df) #>                all obs   #> ———————————————————————— #> High                     #>   Not high    1/4 (25%)  #>   High           0/1     #>   Total      1/6 (16.7%)  # Passing of statistics function and formatting arguments. df2 <- data.frame(   ID = as.character(c(1, 2, 3, 4)),   RANGE = factor(c(\"NORMAL\", \"LOW\", \"HIGH\", \"HIGH\")),   BLRANGE = factor(c(\"LOW\", \"HIGH\", \"HIGH\", \"NORMAL\")) )  basic_table() %>%   count_abnormal_by_baseline(     var = \"RANGE\",     abnormal = c(Low = \"LOW\"),     variables = list(id = \"ID\", baseline = \"BLRANGE\"),     .formats = c(fraction = \"xx / xx\"),     .indent_mods = c(fraction = 2L)   ) %>%   build_table(df2) #>                 all obs #> ——————————————————————— #> Low                     #>       Not low    1 / 3  #>       Low        0 / 1  #>       Total      1 / 4"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with marked laboratory abnormalities — abnormal_by_marked","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"analyze function count_abnormal_by_marked() creates layout element count patients marked laboratory abnormalities direction abnormality, categorized parameter value. function analyzes primary analysis variable var indicates whether single, replicated, last marked laboratory abnormality observed. Levels var include marked lab abnormality (single last_replicated) can supplied via category parameter. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, direction (defaults abn_dir), variable indicate abnormality directions. combination param direction levels, marked lab abnormality counts calculated follows: Single, last & Last replicated: number patients Single, last Last replicated values, respectively. : number patients either single replicated marked abnormalities. Fractions calculated dividing counts number patients least one valid measurement recorded analysis. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable direction.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"count_abnormal_by_marked(   lyt,   var,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )  a_count_abnormal_by_marked(   df,   .var = \"AVALCAT1\",   .spl_context,   category = list(single = \"SINGLE\", last_replicated = c(\"LAST\", \"REPLICATED\")),   variables = list(id = \"USUBJID\", param = \"PARAM\", direction = \"abn_dir\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"lyt (PreDataTableLayouts) layout analyses added . category (list) list different marked category names single last replicated. variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_marked() table layout. s_count_abnormal_by_marked() returns statistic count_fraction Single, last, Last replicated, results. a_count_abnormal_by_marked() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"count_abnormal_by_marked(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_marked(): Statistics function patients marked lab abnormalities. a_count_abnormal_by_marked(): Formatted analysis function used afun count_abnormal_by_marked().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"Single, last Last replicated levels mutually exclusive. patient abnormalities meet Single, last Last replicated criteria, patient counted Last replicated category.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_marked.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with marked laboratory abnormalities — abnormal_by_marked","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(rep(1, 5), rep(2, 5), rep(1, 5), rep(2, 5))),   ARMCD = factor(c(rep(\"ARM A\", 5), rep(\"ARM B\", 5), rep(\"ARM A\", 5), rep(\"ARM B\", 5))),   ANRIND = factor(c(     \"NORMAL\", \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"HIGH\",     \"HIGH\", \"HIGH\", \"HIGH HIGH\", \"NORMAL\", \"HIGH HIGH\", \"NORMAL\", \"LOW\", \"LOW\", \"LOW LOW\", \"LOW\",     \"LOW\", \"LOW\", \"LOW LOW\", \"NORMAL\", \"LOW LOW\"   )),   ONTRTFL = rep(c(\"\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\", \"Y\"), 2),   PARAMCD = factor(c(rep(\"CRP\", 10), rep(\"ALT\", 10))),   AVALCAT1 = factor(rep(c(\"\", \"\", \"\", \"SINGLE\", \"REPLICATED\", \"\", \"\", \"LAST\", \"\", \"SINGLE\"), 2)),   stringsAsFactors = FALSE )  df <- df %>%   mutate(abn_dir = factor(     case_when(       ANRIND == \"LOW LOW\" ~ \"Low\",       ANRIND == \"HIGH HIGH\" ~ \"High\",       TRUE ~ \"\"     ),     levels = c(\"Low\", \"High\")   ))  # Select only post-baseline records. df <- df %>% filter(ONTRTFL == \"Y\") df_crp <- df %>%   filter(PARAMCD == \"CRP\") %>%   droplevels() full_parent_df <- list(df_crp, \"not_needed\") cur_col_subset <- list(rep(TRUE, nrow(df_crp)), \"not_needed\") spl_context <- data.frame(   split = c(\"PARAMCD\", \"GRADE_DIR\"),   full_parent_df = I(full_parent_df),   cur_col_subset = I(cur_col_subset) )  map <- unique(   df[df$abn_dir %in% c(\"Low\", \"High\") & df$AVALCAT1 != \"\", c(\"PARAMCD\", \"abn_dir\")] ) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAMCD, abn_dir)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_to_map(map)   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAMCD\") %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = \"unique_count\"   ) %>%   split_rows_by(     \"abn_dir\",     split_fun = trim_levels_in_group(\"abn_dir\")   ) %>%   count_abnormal_by_marked(     var = \"AVALCAT1\",     variables = list(       id = \"USUBJID\",       param = \"PARAMCD\",       direction = \"abn_dir\"     )   ) %>%   build_table(df = df) #>                           ARM A      ARM B   #> ———————————————————————————————————————————— #> ALT (n)                     1          1     #>   Low                                        #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%) #> CRP (n)                     1          1     #>   High                                       #>     Single, not last     1 (100%)      0     #>     Last or replicated      0       1 (100%) #>     Any Abnormality      1 (100%)   1 (100%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"analyze function count_abnormal_by_worst_grade() creates layout element count patients highest (worst) analysis toxicity grade post-baseline direction, categorized parameter value. function analyzes primary analysis variable var indicates toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, param (defaults PARAM), variable indicate parameter values, grade_dir (defaults GRADE_DIR), variable indicate directions (e.g. High Low) toxicity grade supplied var. combination param grade_dir levels, patient counts worst grade calculated follows: 1 4: number patients worst grades 1-4, respectively. : number patients least one abnormality (.e. grade 0). Fractions calculated dividing counts number patients least one valid measurement recorded treatment. Pre-processing crucial using function can done automatically using h_adlb_abnormal_by_worst_grade() helper function. See description function details necessary pre-processing steps. Prior using function table layout must use rtables::split_rows_by() create two row splits, one variable param one variable grade_dir.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"count_abnormal_by_worst_grade(   lyt,   var,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )  a_count_abnormal_by_worst_grade(   df,   .var = \"GRADE_ANL\",   .spl_context,   variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .spl_context (data.frame) gives information ancestor split states passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_by_worst_grade() table layout. s_count_abnormal_by_worst_grade() returns single statistic count_fraction grades 1 4 \"\" results. a_count_abnormal_by_worst_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"count_abnormal_by_worst_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_by_worst_grade(): Statistics function counts patients worst grade. a_count_abnormal_by_worst_grade(): Formatted analysis function used afun count_abnormal_by_worst_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients by most extreme post-baseline toxicity grade per direction of abnormality — abnormal_by_worst_grade","text":"","code":"library(dplyr) library(forcats) adlb <- tern_ex_adlb  # Data is modified in order to have some parameters with grades only in one direction # and simulate the real data. adlb$ATOXGR[adlb$PARAMCD == \"ALT\" & adlb$ATOXGR %in% c(\"1\", \"2\", \"3\", \"4\")] <- \"-1\" adlb$ANRIND[adlb$PARAMCD == \"ALT\" & adlb$ANRIND == \"HIGH\"] <- \"LOW\" adlb$WGRHIFL[adlb$PARAMCD == \"ALT\"] <- \"\"  adlb$ATOXGR[adlb$PARAMCD == \"IGA\" & adlb$ATOXGR %in% c(\"-1\", \"-2\", \"-3\", \"-4\")] <- \"1\" adlb$ANRIND[adlb$PARAMCD == \"IGA\" & adlb$ANRIND == \"LOW\"] <- \"HIGH\" adlb$WGRLOFL[adlb$PARAMCD == \"IGA\"] <- \"\"  # Pre-processing adlb_f <- adlb %>% h_adlb_abnormal_by_worst_grade()  # Map excludes records without abnormal grade since they should not be displayed # in the table. map <- unique(adlb_f[adlb_f$GRADE_DIR != \"ZERO\", c(\"PARAM\", \"GRADE_DIR\", \"GRADE_ANL\")]) %>%   lapply(as.character) %>%   as.data.frame() %>%   arrange(PARAM, desc(GRADE_DIR), GRADE_ANL)  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   split_rows_by(\"PARAM\") %>%   split_rows_by(\"GRADE_DIR\", split_fun = trim_levels_to_map(map)) %>%   count_abnormal_by_worst_grade(     var = \"GRADE_ANL\",     variables = list(id = \"USUBJID\", param = \"PARAM\", grade_dir = \"GRADE_DIR\")   ) %>%   build_table(df = adlb_f) #>                                          ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————————————— #> Alanine Aminotransferase Measurement                                        #>   LOW                                                                       #>     1                                  12 (17.4%)    5 (6.8%)    8 (13.8%)  #>     2                                   9 (13%)     13 (17.8%)   6 (10.3%)  #>     3                                   6 (8.7%)     4 (5.5%)    6 (10.3%)  #>     4                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     Any                                34 (49.3%)   29 (39.7%)   26 (44.8%) #> C-Reactive Protein Measurement                                              #>   LOW                                                                       #>     1                                  11 (15.9%)   12 (16.4%)   7 (12.1%)  #>     2                                  8 (11.6%)     2 (2.7%)    6 (10.3%)  #>     3                                   4 (5.8%)    9 (12.3%)    6 (10.3%)  #>     4                                  7 (10.1%)     6 (8.2%)     4 (6.9%)  #>     Any                                30 (43.5%)   29 (39.7%)   23 (39.7%) #>   HIGH                                                                      #>     1                                  8 (11.6%)    11 (15.1%)    2 (3.4%)  #>     2                                   9 (13%)     11 (15.1%)    11 (19%)  #>     3                                  14 (20.3%)   10 (13.7%)    5 (8.6%)  #>     4                                   2 (2.9%)     4 (5.5%)    6 (10.3%)  #>     Any                                33 (47.8%)   36 (49.3%)   24 (41.4%) #> Immunoglobulin A Measurement                                                #>   HIGH                                                                      #>     1                                  7 (10.1%)     7 (9.6%)    6 (10.3%)  #>     2                                  8 (11.6%)     6 (8.2%)    8 (13.8%)  #>     3                                  7 (10.1%)     5 (6.8%)    9 (15.5%)  #>     4                                   6 (8.7%)     2 (2.7%)     3 (5.2%)  #>     Any                                28 (40.6%)   20 (27.4%)   26 (44.8%)"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"analyze function count_abnormal_lab_worsen_by_baseline() creates layout element count patients analysis toxicity grades worsened baseline, categorized highest (worst) grade post-baseline. function analyzes primary analysis variable var indicates analysis toxicity grades. Additional analysis variables can supplied list via variables parameter id (defaults USUBJID), variable indicate unique subject identifiers, baseline_var (defaults BTOXGR), variable indicate baseline toxicity grades, direction_var (defaults GRADDIR), variable indicate toxicity grade directions interest include (e.g. \"H\" (high), \"L\" (low), \"B\" ()). direction(s) specified direction_var, patient counts worst grade patients worsened baseline calculated follows: 1 4: number patients worsened baseline grades worst grades 1-4, respectively. : total number patients worsened baseline grades. Fractions calculated dividing counts number patients analysis toxicity grades worsened baseline toxicity grades treatment. Prior using function table layout must use rtables::split_rows_by() create row split variable direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"count_abnormal_lab_worsen_by_baseline(   lyt,   var,   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )  a_count_abnormal_lab_worsen_by_baseline(   df,   .var = \"ATOXGR\",   variables = list(id = \"USUBJID\", baseline_var = \"BTOXGR\", direction_var = \"GRADDR\") )"},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables including: id (string) subject variable name. baseline_var (string) name data column containing baseline toxicity variable. direction_var (string) see direction_var details. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_abnormal_lab_worsen_by_baseline() table layout. s_count_abnormal_lab_worsen_by_baseline() returns counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\". a_count_abnormal_lab_worsen_by_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"count_abnormal_lab_worsen_by_baseline(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_abnormal_lab_worsen_by_baseline(): Statistics function patients whose worst post-baseline lab grades worse baseline grades. a_count_abnormal_lab_worsen_by_baseline(): Formatted analysis function used afun count_abnormal_lab_worsen_by_baseline().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/abnormal_by_worst_grade_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patients with toxicity grades that have worsened from baseline by highest grade post-baseline — abnormal_by_worst_grade_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  basic_table() %>%   split_cols_by(\"ARMCD\") %>%   add_colcounts() %>%   split_rows_by(\"PARAMCD\") %>%   split_rows_by(\"GRADDR\") %>%   count_abnormal_lab_worsen_by_baseline(     var = \"ATOXGR\",     variables = list(       id = \"USUBJID\",       baseline_var = \"BTOXGR\",       direction_var = \"GRADDR\"     )   ) %>%   append_topleft(\"Direction of Abnormality\") %>%   build_table(df = df, alt_counts_df = tern_ex_adsl) #>                                ARM A           ARM B           ARM C     #> Direction of Abnormality      (N=69)          (N=73)          (N=58)     #> ———————————————————————————————————————————————————————————————————————— #> IGA                                                                      #>   High                                                                   #>     1                       6/63 (9.5%)     6/64 (9.4%)      4/50 (8%)   #>     2                      8/64 (12.5%)     5/67 (7.5%)    8/53 (15.1%)  #>     3                      7/66 (10.6%)     5/68 (7.4%)    9/57 (15.8%)  #>     4                       6/68 (8.8%)     2/72 (2.8%)     3/58 (5.2%)  #>     Any                    27/68 (39.7%)    18/72 (25%)    24/58 (41.4%) #> ALT                                                                      #>   High                                                                   #>     1                      7/63 (11.1%)     6/62 (9.7%)     2/48 (4.2%)  #>     2                       12/63 (19%)      4/67 (6%)      11/50 (22%)  #>     3                       4/65 (6.2%)    11/71 (15.5%)   7/56 (12.5%)  #>     4                       1/67 (1.5%)    8/71 (11.3%)      4/57 (7%)   #>     Any                    24/67 (35.8%)   29/71 (40.8%)   24/57 (42.1%) #>   Low                                                                    #>     1                      12/67 (17.9%)    4/66 (6.1%)    7/52 (13.5%)  #>     2                      9/68 (13.2%)    12/69 (17.4%)   6/55 (10.9%)  #>     3                       6/69 (8.7%)     4/71 (5.6%)     5/56 (8.9%)  #>     4                      7/69 (10.1%)     7/73 (9.6%)    6/58 (10.3%)  #>     Any                    34/69 (49.3%)    27/73 (37%)    24/58 (41.4%) #> CRP                                                                      #>   Low                                                                    #>     1                      11/66 (16.7%)   10/67 (14.9%)    4/47 (8.5%)  #>     2                      8/66 (12.1%)     1/70 (1.4%)     6/50 (12%)   #>     3                       4/68 (5.9%)    9/70 (12.9%)     5/53 (9.4%)  #>     4                      7/69 (10.1%)     6/72 (8.3%)     4/55 (7.3%)  #>     Any                    30/69 (43.5%)   26/72 (36.1%)   19/55 (34.5%)"},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Split function to configure risk difference column — add_riskdiff","title":"Split function to configure risk difference column — add_riskdiff","text":"Wrapper function rtables::add_combo_levels() configures settings risk difference column added rtables object. add risk difference column table, function used split_fun calls rtables::split_cols_by(), followed setting argument riskdiff TRUE following analyze function calls.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"add_riskdiff(   arm_x,   arm_y,   col_label = paste0(\"Risk Difference (%) (95% CI)\", if (length(arm_y) > 1)     paste0(\"\\n\", arm_x, \" vs. \", arm_y)),   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split function to configure risk difference column — add_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split function to configure risk difference column — add_riskdiff","text":"closure suitable use split function (split_fun) within rtables::split_cols_by() creating table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/add_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split function to configure risk difference column — add_riskdiff","text":"","code":"adae <- tern_ex_adae adae$AESEV <- factor(adae$AESEV)  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_riskdiff(arm_x = \"ARM A\", arm_y = c(\"ARM B\", \"ARM C\"))) %>%   count_occurrences_by_grade(     var = \"AESEV\",     riskdiff = TRUE   )  tbl <- build_table(lyt, df = adae) tbl #>                                                   Risk Difference (%) (95% CI)   Risk Difference (%) (95% CI) #>              ARM A        ARM B        ARM C            ARM A vs. ARM B                ARM A vs. ARM C        #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> MILD        6 (3.0%)     4 (2.3%)     2 (1.2%)          0.7 (-2.5 - 3.9)               1.7 (-1.2 - 4.6)       #> MODERATE   19 (9.4%)    15 (8.5%)    14 (8.6%)          0.9 (-4.8 - 6.7)               0.8 (-5.1 - 6.7)       #> SEVERE     34 (16.8%)   38 (21.5%)   32 (19.8%)        -4.6 (-12.6 - 3.3)             -2.9 (-10.9 - 5.1)"},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":null,"dir":"Reference","previous_headings":"","what":"Layout-creating function to add row total counts — add_rowcounts","title":"Layout-creating function to add row total counts — add_rowcounts","text":"works analogously rtables::add_colcounts() rows. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"add_rowcounts(lyt, alt_counts = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Layout-creating function to add row total counts — add_rowcounts","text":"lyt (PreDataTableLayouts) layout analyses added . alt_counts (flag) whether row counts taken alt_counts_df (TRUE) df (FALSE). Defaults FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Layout-creating function to add row total counts — add_rowcounts","text":"modified layout latest row split labels now row-wise total counts (.e. without column-based subsetting) attached parentheses.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Layout-creating function to add row total counts — add_rowcounts","text":"Row count values contained row count rows displayed considered zero rows default pruning.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/add_rowcounts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Layout-creating function to add row total counts — add_rowcounts","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"RACE\", split_fun = drop_split_levels) %>%   add_rowcounts() %>%   analyze(\"AGE\", afun = list_wrap_x(summary), format = \"xx.xx\") %>%   build_table(DM) #>                                    A: Drug X   B: Placebo   C: Combination #>                                     (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————————————————————————————————— #> ASIAN (N=231)                                                              #>   Min.                               20.00       21.00          22.00      #>   1st Qu.                            29.00       28.00          30.00      #>   Median                             33.00       32.50          33.50      #>   Mean                               34.20       32.68          34.63      #>   3rd Qu.                            38.50       36.00          38.00      #>   Max.                               58.00       55.00          53.00      #> BLACK OR AFRICAN AMERICAN (N=79)                                           #>   Min.                               23.00       21.00          24.00      #>   1st Qu.                            29.00       28.75          29.00      #>   Median                             33.00       30.00          32.00      #>   Mean                               34.68       31.71          34.00      #>   3rd Qu.                            37.25       36.25          39.00      #>   Max.                               60.00       42.00          51.00      #> WHITE (N=46)                                                               #>   Min.                               30.00       25.00          28.00      #>   1st Qu.                            38.00       31.00          30.25      #>   Median                             40.50       37.50          35.00      #>   Mean                               39.36       36.93          35.11      #>   3rd Qu.                            43.50       40.00          37.50      #>   Max.                               47.00       55.00          47.00"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for adverse event baskets — aesi_label","text":"","code":"aesi_label(aesi, scope = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for adverse event baskets — aesi_label","text":"aesi (character) vector standardized MedDRA query name (e.g. SMQxxNAM) customized query name (e.g. CQxxNAM). scope (character) vector scope query (e.g. SMQxxSC).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for adverse event baskets — aesi_label","text":"string standard label AE basket.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/aesi_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Labels for adverse event baskets — aesi_label","text":"","code":"adae <- tern_ex_adae  # Standardized query label includes scope. aesi_label(adae$SMQ01NAM, scope = adae$SMQ01SC) #> [1] \"C.1.1.1.3/B.2.2.3.1 aesi (BROAD)\"  # Customized query label. aesi_label(adae$CQ01NAM) #> [1] \"D.2.1.5.3/A.1.1.1.1 aesi\""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Analysis function to calculate risk difference column values — afun_riskdiff","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"risk difference column, function uses statistics function associated afun calculates risk difference values arm X (reference group) arm Y. arms specified configuring risk difference column done using add_riskdiff() split function previous call rtables::split_cols_by(). columns, applies afun usual. function utilizes stat_propdiff_ci() function perform risk difference calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"","code":"afun_riskdiff(   df,   labelstr = \"\",   .var,   .N_col,   .N_row,   .df_row,   .spl_context,   .all_col_counts,   .stats,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   afun,   s_args = list() )"},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .df_row (data.frame) data frame across columns given row split. .spl_context (data.frame) gives information ancestor split states passed rtables. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. afun (named list) named list containing one name-value pair name corresponds name statistics function used calculations value corresponding analysis function. s_args (named list) additional arguments passed statistics function analysis function supplied afun.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analysis function to calculate risk difference column values — afun_riskdiff","text":"list formatted rtables::CellValue().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Get selected statistics names — afun_selected_stats","title":"Get selected statistics names — afun_selected_stats","text":"Helper function used creating afun.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get selected statistics names — afun_selected_stats","text":"","code":"afun_selected_stats(.stats, all_stats)"},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get selected statistics names — afun_selected_stats","text":".stats (vector NULL) input layout creating function. Note NULL means context default statistics used. all_stats (character) statistics can selected potentially.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/afun_selected_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get selected statistics names — afun_selected_stats","text":"character vector selected statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_colvars_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions in columns — analyze_colvars_functions","title":"Analyze functions in columns — analyze_colvars_functions","text":"functions wrappers rtables::analyze_colvars() apply corresponding tern statistics functions add analysis given table layout. particular, functions designed analysis methods split different columns. analyze_vars_in_cols(): fundamental tabulation analysis methods onto columns. words, analysis methods defined column space, .e. become column labels. changing variable vector, list functions can applied different variables, caveat number statistical functions. tabulate_rsp_subgroups(): similarly analyze_vars_in_cols, function combines analyze_colvars summarize_row_groups compact way produce standard tables show analysis methods columns. tabulate_survival_subgroups(): function similar , used tables. analyze_patients_exposure_in_cols(): based analyze_colvars. needs summarize_patients_exposure_in_cols() leverage nesting label rows analysis rtables::summarize_row_groups(). summarize_coxreg(): generally based rtables::summarize_row_groups(), behaves similarly tabulate_* functions described designed provide specific standard tables may contain nested structure combination summarize_row_groups() rtables::analyze_colvars().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze functions — analyze_functions","title":"Analyze functions — analyze_functions","text":"functions wrappers rtables::analyze() apply corresponding tern statistics functions add analysis given table layout: analyze_num_patients() analyze_vars() compare_vars() count_abnormal() count_abnormal_by_baseline() count_abnormal_by_marked() count_abnormal_by_worst_grade() count_cumulative() count_missed_doses() count_occurrences() count_occurrences_by_grade() count_patients_events_in_cols() count_patients_with_event() count_patients_with_flags() count_values() coxph_pairwise() estimate_incidence_rate() estimate_multinomial_rsp() estimate_odds_ratio() estimate_proportion() estimate_proportion_diff() summarize_ancova() summarize_colvars(): even function uses rtables::analyze_colvars(), applies analysis methods different rows one variables split different columns. comparison, analyze_colvars_functions leverage analyze_colvars context split rows analysis methods columns. summarize_change() surv_time() surv_timepoint() test_proportion_diff()","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze variables — analyze_variables","title":"Analyze variables — analyze_variables","text":"analyze function analyze_vars() creates layout element summarize one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\") non-numeric variables running get_stats(\"analyze_vars_counts\"). Use .stats parameter specify statistics include output summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze variables — analyze_variables","text":"","code":"analyze_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_summary(x, na.rm = TRUE, denom, .N_row, .N_col, .var, ...)  # S3 method for class 'numeric' s_summary(   x,   na.rm = TRUE,   denom,   .N_row,   .N_col,   .var,   control = control_analyze_vars(),   ... )  # S3 method for class 'factor' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   ... )  # S3 method for class 'character' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_summary(   x,   na.rm = TRUE,   denom = c(\"n\", \"N_row\", \"N_col\"),   .N_row,   .N_col,   ... )  a_summary(   x,   .N_col,   .N_row,   .var = NULL,   .df_row = NULL,   .ref_group = NULL,   .in_ref_col = FALSE,   compare = FALSE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na.rm = TRUE,   na_str = default_na_str(),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze variables — analyze_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_summary(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .var (string) single variable name passed rtables requested statistics function. control (list) parameters descriptive statistics details, specified using helper function control_analyze_vars(). possible parameter options : conf_level (proportion) confidence level interval mean median. quantiles (numeric(2)) vector length two specify quantiles. quantile_type (numeric(1)) 1 9 selecting quantile algorithms used. See type stats::quantile(). test_mean (numeric(1)) value test mean null hypothesis calculating p-value. verbose (flag) defaults TRUE, prints warnings messages. mainly used print information factor casting. .df_row (data.frame) data frame across columns given row split. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. compare (flag) whether comparison statistics analyzed instead summary statistics (compare = TRUE adds pval statistic comparing reference group).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze variables — analyze_variables","text":"analyze_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_summary() table layout. s_summary() returns different statistics depending class x. x class numeric, returns list following named numeric items: n: length() x. sum: sum() x. mean: mean() x. sd: stats::sd() x. se: standard error x mean, .e.: (sd(x) / sqrt(length(x))). mean_sd: mean() stats::sd() x. mean_se: mean() x standard error (see ). mean_ci: CI mean x (stat_mean_ci()). mean_sei: SE interval mean x, .e.: (mean() -/+ stats::sd() / sqrt()). mean_sdi: SD interval mean x, .e.: (mean() -/+ stats::sd()). mean_pval: two-sided p-value mean x (stat_mean_pval()). median: stats::median() x. mad: median absolute deviation x, .e.: (stats::median() xc, xc = x - stats::median()). median_ci: CI median x (stat_median_ci()). quantiles: Two sample quantiles x (stats::quantile()). iqr: stats::IQR() x. range: range_noinf() x. min: max() x. max: min() x. median_range: median() range_noinf() x. cv: coefficient variation x, .e.: (stats::sd() / mean() * 100). geom_mean: geometric mean x, .e.: (exp(mean(log(x)))). geom_cv: geometric coefficient variation x, .e.: (sqrt(exp(sd(log(x)) ^ 2) - 1) * 100). x class factor converted character, returns list named numeric items: n: length() x. count: list number cases level factor x. count_fraction: Similar count also includes proportion cases level factor x relative denominator, NA denominator zero. x class logical, returns list named numeric items: n: length() x (possibly removing NAs). count: Count TRUE x. count_fraction: Count proportion TRUE x relative denominator, NA denominator zero. Note NAs x never counted leading NA . a_summary() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Analyze variables — analyze_variables","text":"Automatic digit formatting: number digits display can automatically determined analyzed variable(s) (vars) certain statistics setting statistic format \"auto\" .formats. utilizes format_auto() formatting function. Note data current row & variable (columns) considered (.df_row[[.var]], see rtables::additional_fun_params) whole dataset.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze variables — analyze_variables","text":"analyze_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_summary(): S3 generic function produces variable summary. s_summary(numeric): Method numeric class. s_summary(factor): Method factor class. s_summary(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_summary(logical): Method logical class. a_summary(): Formatted analysis function used afun analyze_vars() compare_vars() cfun summarize_colvars().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze variables — analyze_variables","text":"x empty vector, NA returned. expected feature return rcell content rtables intersection column row delimits empty data selection. mean function applied empty vector, NA returned instead NaN, latter standard behavior R. x empty factor, list still returned counts one element per factor level. levels x, function fails. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. Automatic conversion character factor guarantee table can generated correctly. particular sparse tables likely can fail. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table(). use comparison (additional p-value statistic), parameter compare must set TRUE. Ensure either NA values converted explicit NA level NA values left .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze variables — analyze_variables","text":"","code":"## Fabricated dataset. dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVAL    = c(9:1, rep(NA, 9)) )  # `analyze_vars()` in `rtables` pipelines ## Default output within a `rtables` pipeline. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  build_table(l, df = dta_test) #>                   A           B       C  #> ———————————————————————————————————————— #> V1                                       #>   n               2           1       0  #>   Mean (SD)   7.5 (2.1)   3.0 (NA)    NA #>   Median         7.5         3.0      NA #>   Min - Max   6.0 - 9.0   3.0 - 3.0   NA #> V2                                       #>   n               2           1       0  #>   Mean (SD)   6.5 (2.1)   2.0 (NA)    NA #>   Median         6.5         2.0      NA #>   Min - Max   5.0 - 8.0   2.0 - 2.0   NA #> V3                                       #>   n               2           1       0  #>   Mean (SD)   5.5 (2.1)   1.0 (NA)    NA #>   Median         5.5         1.0      NA #>   Min - Max   4.0 - 7.0   1.0 - 1.0   NA  ## Select and format statistics output. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(     vars = \"AVAL\",     .stats = c(\"n\", \"mean_sd\", \"quantiles\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\", quantiles = c(\"Q1 - Q3\"))   )  build_table(l, df = dta_test) #>                  A           B       C  #> ——————————————————————————————————————— #> V1                                      #>   n              2           1       0  #>   Mean, SD   7.5, 2.1     3.0, NA    NA #>   Q1 - Q3    6.0 - 9.0   3.0 - 3.0   NA #> V2                                      #>   n              2           1       0  #>   Mean, SD   6.5, 2.1     2.0, NA    NA #>   Q1 - Q3    5.0 - 8.0   2.0 - 2.0   NA #> V3                                      #>   n              2           1       0  #>   Mean, SD   5.5, 2.1     1.0, NA    NA #>   Q1 - Q3    4.0 - 7.0   1.0 - 1.0   NA  ## Use arguments interpreted by `s_summary`. l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\", na.rm = FALSE)  build_table(l, df = dta_test) #>                   A       B    C  #> ————————————————————————————————— #> V1                                #>   n               2       2    2  #>   Mean (SD)   7.5 (2.1)   NA   NA #>   Median         7.5      NA   NA #>   Min - Max   6.0 - 9.0   NA   NA #> V2                                #>   n               2       2    2  #>   Mean (SD)   6.5 (2.1)   NA   NA #>   Median         6.5      NA   NA #>   Min - Max   5.0 - 8.0   NA   NA #> V3                                #>   n               2       2    2  #>   Mean (SD)   5.5 (2.1)   NA   NA #>   Median         5.5      NA   NA #>   Min - Max   4.0 - 7.0   NA   NA  ## Handle `NA` levels first when summarizing factors. dta_test$AVISIT <- NA_character_ dta_test <- df_explicit_na(dta_test) l <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   analyze_vars(vars = \"AVISIT\", na.rm = FALSE)  build_table(l, df = dta_test) #>                A          B          C     #> —————————————————————————————————————————— #> n              6          6          6     #> <Missing>   6 (100%)   6 (100%)   6 (100%)  # auto format dt <- data.frame(\"VAR\" = c(0.001, 0.2, 0.0011000, 3, 4)) basic_table() %>%   analyze_vars(     vars = \"VAR\",     .stats = c(\"n\", \"mean\", \"mean_sd\", \"range\"),     .formats = c(\"mean_sd\" = \"auto\", \"range\" = \"auto\")   ) %>%   build_table(dt) #>                  all obs      #> ————————————————————————————— #> n                   5         #> Mean               1.4        #> Mean (SD)   1.44042 (1.91481) #> Min - Max    0.0010 - 4.0000   # `s_summary.numeric`  ## Basic usage: empty numeric returns NA-filled items. s_summary(numeric()) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>   ## Management of NA values. x <- c(NA_real_, 1) s_summary(x, na.rm = TRUE) #> $n #> n  #> 1  #>  #> $sum #> sum  #>   1  #>  #> $mean #> mean  #>    1  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>    1   NA  #>  #> $mean_se #> mean   se  #>    1   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>      1  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             1  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   0  #>  #> $range #> min max  #>   1   1  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   1  #>  #> $median_range #> median    min    max  #>      1      1      1  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>         1  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  s_summary(x, na.rm = FALSE) #> $n #> n  #> 2  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>        NA  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>   x <- c(NA_real_, 1, 2) s_summary(x, stats = NULL) #> $n #> n  #> 2  #>  #> $sum #> sum  #>   3  #>  #> $mean #> mean  #>  1.5  #>  #> $sd #>        sd  #> 0.7071068  #>  #> $se #>  se  #> 0.5  #>  #> $mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $mean_se #> mean   se  #>  1.5  0.5  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>    1.5  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>   1  #>  #> $range #> min max  #>   1   2  #>  #> $min #> min  #>   1  #>  #> $max #> max  #>   2  #>  #> $median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 47.14045  #>  #> $geom_mean #> geom_mean  #>  1.414214  #>  #> $geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 52.10922  #>   ## Benefits in `rtables` contructions: dta_test <- data.frame(   Group = rep(LETTERS[1:3], each = 2),   sub_group = rep(letters[1:2], each = 3),   x = 1:6 )  ## The summary obtained in with `rtables`: basic_table() %>%   split_cols_by(var = \"Group\") %>%   split_rows_by(var = \"sub_group\") %>%   analyze(vars = \"x\", afun = s_summary) %>%   build_table(df = dta_test) #>                                                  A                        B                       C                   #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> a                                                                                                                     #>   n                                              2                        1                       0                   #>   sum                                            3                        3                       NA                  #>   mean                                          1.5                       3                       NA                  #>   sd                                     0.707106781186548               NA                       NA                  #>   se                                            0.5                      NA                       NA                  #>   mean_sd                              1.5, 0.707106781186548           3, NA                     NA                  #>   mean_se                                     1.5, 0.5                  3, NA                     NA                  #>   Mean 95% CI                   -4.85310236808735, 7.85310236808735      NA                       NA                  #>   Mean -/+ 1xSE                                 1, 2                     NA                       NA                  #>   Mean -/+ 1xSD                 0.792893218813452, 2.20710678118655      NA                       NA                  #>   Mean p-value (H0: mean = 0)            0.204832764699133               NA                       NA                  #>   median                                        1.5                       3                       NA                  #>   mad                                            0                        0                       NA                  #>   Median 95% CI                                  NA                      NA                       NA                  #>   25% and 75%-ile                               1, 2                    3, 3                      NA                  #>   iqr                                            1                        0                       NA                  #>   range                                         1, 2                    3, 3                      NA                  #>   min                                            1                        3                       NA                  #>   max                                            2                        3                       NA                  #>   Median (Min - Max)                         1.5, 1, 2                 3, 3, 3                    NA                  #>   cv                                      47.1404520791032               NA                       NA                  #>   geom_mean                               1.41421356237309                3                       NA                  #>   Geometric Mean 95% CI         0.0172997815631007, 115.608396135236     NA                       NA                  #>   geom_cv                                 52.1092246837487               NA                       NA                  #> b                                                                                                                     #>   n                                              0                        1                       2                   #>   sum                                            NA                       4                       11                  #>   mean                                           NA                       4                      5.5                  #>   sd                                             NA                      NA               0.707106781186548           #>   se                                             NA                      NA                      0.5                  #>   mean_sd                                        NA                     4, NA           5.5, 0.707106781186548        #>   mean_se                                        NA                     4, NA                  5.5, 0.5               #>   Mean 95% CI                                    NA                      NA      -0.853102368087347, 11.8531023680873 #>   Mean -/+ 1xSE                                  NA                      NA                      5, 6                 #>   Mean -/+ 1xSD                                  NA                      NA       4.79289321881345, 6.20710678118655  #>   Mean p-value (H0: mean = 0)                    NA                      NA               0.0577158767526089          #>   median                                         NA                       4                      5.5                  #>   mad                                            NA                       0                       0                   #>   Median 95% CI                                  NA                      NA                       NA                  #>   25% and 75%-ile                                NA                     4, 4                     5, 6                 #>   iqr                                            NA                       0                       1                   #>   range                                          NA                     4, 4                     5, 6                 #>   min                                            NA                       4                       5                   #>   max                                            NA                       4                       6                   #>   Median (Min - Max)                             NA                    4, 4, 4                5.5, 5, 6               #>   cv                                             NA                      NA                12.8564869306645           #>   geom_mean                                      NA                       4                5.47722557505166           #>   Geometric Mean 95% CI                          NA                      NA       1.71994304449266, 17.4424380482025  #>   geom_cv                                        NA                      NA                12.945835316564             ## By comparison with `lapply`: X <- split(dta_test, f = with(dta_test, interaction(Group, sub_group))) lapply(X, function(x) s_summary(x$x)) #> $A.a #> $A.a$n #> n  #> 2  #>  #> $A.a$sum #> sum  #>   3  #>  #> $A.a$mean #> mean  #>  1.5  #>  #> $A.a$sd #>        sd  #> 0.7071068  #>  #> $A.a$se #>  se  #> 0.5  #>  #> $A.a$mean_sd #>      mean        sd  #> 1.5000000 0.7071068  #>  #> $A.a$mean_se #> mean   se  #>  1.5  0.5  #>  #> $A.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>   -4.853102    7.853102  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>            1            2  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>    0.7928932    2.2071068  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.a$mean_pval #>   p_value  #> 0.2048328  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.a$median #> median  #>    1.5  #>  #> $A.a$mad #> mad  #>   0  #>  #> $A.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.a$quantiles #> quantile_0.25 quantile_0.75  #>             1             2  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.a$iqr #> iqr  #>   1  #>  #> $A.a$range #> min max  #>   1   2  #>  #> $A.a$min #> min  #>   1  #>  #> $A.a$max #> max  #>   2  #>  #> $A.a$median_range #> median    min    max  #>    1.5    1.0    2.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.a$cv #>       cv  #> 47.14045  #>  #> $A.a$geom_mean #> geom_mean  #>  1.414214  #>  #> $A.a$geom_mean_ci #>  mean_ci_lwr  mean_ci_upr  #>   0.01729978 115.60839614  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.a$geom_cv #>  geom_cv  #> 52.10922  #>  #>  #> $B.a #> $B.a$n #> n  #> 1  #>  #> $B.a$sum #> sum  #>   3  #>  #> $B.a$mean #> mean  #>    3  #>  #> $B.a$sd #> sd  #> NA  #>  #> $B.a$se #> se  #> NA  #>  #> $B.a$mean_sd #> mean   sd  #>    3   NA  #>  #> $B.a$mean_se #> mean   se  #>    3   NA  #>  #> $B.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.a$median #> median  #>      3  #>  #> $B.a$mad #> mad  #>   0  #>  #> $B.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.a$quantiles #> quantile_0.25 quantile_0.75  #>             3             3  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.a$iqr #> iqr  #>   0  #>  #> $B.a$range #> min max  #>   3   3  #>  #> $B.a$min #> min  #>   3  #>  #> $B.a$max #> max  #>   3  #>  #> $B.a$median_range #> median    min    max  #>      3      3      3  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.a$cv #> cv  #> NA  #>  #> $B.a$geom_mean #> geom_mean  #>         3  #>  #> $B.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.a$geom_cv #> geom_cv  #>      NA  #>  #>  #> $C.a #> $C.a$n #> n  #> 0  #>  #> $C.a$sum #> sum  #>  NA  #>  #> $C.a$mean #> mean  #>   NA  #>  #> $C.a$sd #> sd  #> NA  #>  #> $C.a$se #> se  #> NA  #>  #> $C.a$mean_sd #> mean   sd  #>   NA   NA  #>  #> $C.a$mean_se #> mean   se  #>   NA   NA  #>  #> $C.a$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.a$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.a$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.a$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.a$median #> median  #>     NA  #>  #> $C.a$mad #> mad  #>  NA  #>  #> $C.a$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.a$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.a$iqr #> iqr  #>  NA  #>  #> $C.a$range #> min max  #>  NA  NA  #>  #> $C.a$min #> min  #>  NA  #>  #> $C.a$max #> max  #>  NA  #>  #> $C.a$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.a$cv #> cv  #> NA  #>  #> $C.a$geom_mean #> geom_mean  #>       NaN  #>  #> $C.a$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.a$geom_cv #> geom_cv  #>      NA  #>  #>  #> $A.b #> $A.b$n #> n  #> 0  #>  #> $A.b$sum #> sum  #>  NA  #>  #> $A.b$mean #> mean  #>   NA  #>  #> $A.b$sd #> sd  #> NA  #>  #> $A.b$se #> se  #> NA  #>  #> $A.b$mean_sd #> mean   sd  #>   NA   NA  #>  #> $A.b$mean_se #> mean   se  #>   NA   NA  #>  #> $A.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $A.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $A.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $A.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $A.b$median #> median  #>     NA  #>  #> $A.b$mad #> mad  #>  NA  #>  #> $A.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $A.b$quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $A.b$iqr #> iqr  #>  NA  #>  #> $A.b$range #> min max  #>  NA  NA  #>  #> $A.b$min #> min  #>  NA  #>  #> $A.b$max #> max  #>  NA  #>  #> $A.b$median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $A.b$cv #> cv  #> NA  #>  #> $A.b$geom_mean #> geom_mean  #>       NaN  #>  #> $A.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $A.b$geom_cv #> geom_cv  #>      NA  #>  #>  #> $B.b #> $B.b$n #> n  #> 1  #>  #> $B.b$sum #> sum  #>   4  #>  #> $B.b$mean #> mean  #>    4  #>  #> $B.b$sd #> sd  #> NA  #>  #> $B.b$se #> se  #> NA  #>  #> $B.b$mean_sd #> mean   sd  #>    4   NA  #>  #> $B.b$mean_se #> mean   se  #>    4   NA  #>  #> $B.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $B.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $B.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $B.b$mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $B.b$median #> median  #>      4  #>  #> $B.b$mad #> mad  #>   0  #>  #> $B.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $B.b$quantiles #> quantile_0.25 quantile_0.75  #>             4             4  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $B.b$iqr #> iqr  #>   0  #>  #> $B.b$range #> min max  #>   4   4  #>  #> $B.b$min #> min  #>   4  #>  #> $B.b$max #> max  #>   4  #>  #> $B.b$median_range #> median    min    max  #>      4      4      4  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $B.b$cv #> cv  #> NA  #>  #> $B.b$geom_mean #> geom_mean  #>         4  #>  #> $B.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $B.b$geom_cv #> geom_cv  #>      NA  #>  #>  #> $C.b #> $C.b$n #> n  #> 2  #>  #> $C.b$sum #> sum  #>  11  #>  #> $C.b$mean #> mean  #>  5.5  #>  #> $C.b$sd #>        sd  #> 0.7071068  #>  #> $C.b$se #>  se  #> 0.5  #>  #> $C.b$mean_sd #>      mean        sd  #> 5.5000000 0.7071068  #>  #> $C.b$mean_se #> mean   se  #>  5.5  0.5  #>  #> $C.b$mean_ci #> mean_ci_lwr mean_ci_upr  #>  -0.8531024  11.8531024  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $C.b$mean_sei #> mean_sei_lwr mean_sei_upr  #>            5            6  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $C.b$mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     4.792893     6.207107  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $C.b$mean_pval #>    p_value  #> 0.05771588  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $C.b$median #> median  #>    5.5  #>  #> $C.b$mad #> mad  #>   0  #>  #> $C.b$median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $C.b$quantiles #> quantile_0.25 quantile_0.75  #>             5             6  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $C.b$iqr #> iqr  #>   1  #>  #> $C.b$range #> min max  #>   5   6  #>  #> $C.b$min #> min  #>   5  #>  #> $C.b$max #> max  #>   6  #>  #> $C.b$median_range #> median    min    max  #>    5.5    5.0    6.0  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $C.b$cv #>       cv  #> 12.85649  #>  #> $C.b$geom_mean #> geom_mean  #>  5.477226  #>  #> $C.b$geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    1.719943   17.442438  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $C.b$geom_cv #>  geom_cv  #> 12.94584  #>  #>   # `s_summary.factor`  ## Basic usage: s_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\"))) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(factor(levels = c(\"a\", \"b\", \"c\"))) #> $n #> [1] 0 #>  #> $count #> $count$a #> [1] 0 #>  #> $count$b #> [1] 0 #>  #> $count$c #> [1] 0 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 0 0 #>  #> $count_fraction$b #> [1] 0 0 #>  #> $count_fraction$c #> [1] 0 0 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     0     0  #>  #> $fraction$b #>   num denom  #>     0     0  #>  #> $fraction$c #>   num denom  #>     0     0  #>  #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- factor(c(NA, \"Female\")) x <- explicit_na(x) s_summary(x, na.rm = TRUE) #> $n #> [1] 1 #>  #> $count #> $count$Female #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1 1 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     1  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 2 #>  #> $count #> $count$Female #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$Female #> [1] 1.0 0.5 #>  #> $count_fraction$`<Missing>` #> [1] 1.0 0.5 #>  #>  #> $fraction #> $fraction$Female #>   num denom  #>     1     2  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     2  #>  #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.3 #>  #> $count_fraction$b #> [1] 1.0 0.1 #>  #> $count_fraction$c #> [1] 1.0 0.1 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    10  #>  #> $fraction$b #>   num denom  #>     1    10  #>  #> $fraction$c #>   num denom  #>     1    10  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.00 0.15 #>  #> $count_fraction$b #> [1] 1.00 0.05 #>  #> $count_fraction$c #> [1] 1.00 0.05 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3    20  #>  #> $fraction$b #>   num denom  #>     1    20  #>  #> $fraction$c #>   num denom  #>     1    20  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.character`  ## Basic usage: s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\"), .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  s_summary(c(\"a\", \"a\", \"b\", \"c\", \"a\", \"\"), .var = \"x\", na.rm = FALSE, verbose = FALSE) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`NA` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`NA` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`NA` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>   # `s_summary.logical`  ## Basic usage: s_summary(c(TRUE, FALSE, TRUE, TRUE)) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>   # Empty factor returns zero-filled items. s_summary(as.logical(c())) #> $n #> [1] 0 #>  #> $count #> [1] 0 #>  #> $count_fraction #> [1] 0 0 #>  #> $n_blq #> [1] 0 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) s_summary(x, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  s_summary(x, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>   ## Different denominators. x <- c(TRUE, FALSE, TRUE, TRUE) s_summary(x, denom = \"N_row\", .N_row = 10L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.0 0.3 #>  #> $n_blq #> [1] 0 #>  s_summary(x, denom = \"N_col\", .N_col = 20L) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.15 #>  #> $n_blq #> [1] 0 #>   a_summary(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              5          0         n #> 2                    count.a              3          0         a #> 3                    count.b              1          0         b #> 4                    count.c              1          0         c #> 5           count_fraction.a        3 (60%)          0         a #> 6           count_fraction.b        1 (20%)          0         b #> 7           count_fraction.c        1 (20%)          0         c #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0         a #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0         b #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0         c #> 11                fraction.a    3/5 (60.0%)          0         a #> 12                fraction.b    1/5 (20.0%)          0         b #> 13                fraction.c    1/5 (20.0%)          0         c #> 14                     n_blq              0          0     n_blq a_summary(   factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")),   .ref_group = factor(c(\"a\", \"a\", \"b\", \"c\")), compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              5          0 #> 2                    count.a              3          0 #> 3                    count.b              1          0 #> 4                    count.c              1          0 #> 5           count_fraction.a        3 (60%)          0 #> 6           count_fraction.b        1 (20%)          0 #> 7           count_fraction.c        1 (20%)          0 #> 8  count_fraction_fixed_dp.a      3 (60.0%)          0 #> 9  count_fraction_fixed_dp.b      1 (20.0%)          0 #> 10 count_fraction_fixed_dp.c      1 (20.0%)          0 #> 11                fraction.a    3/5 (60.0%)          0 #> 12                fraction.b    1/5 (20.0%)          0 #> 13                fraction.c    1/5 (20.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9560          0 #>                     row_label #> 1                           n #> 2                           a #> 3                           b #> 4                           c #> 5                           a #> 6                           b #> 7                           c #> 8                           a #> 9                           b #> 10                          c #> 11                          a #> 12                          b #> 13                          c #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(\"A\", \"B\", \"A\", \"C\"), .var = \"x\", .N_col = 10, .N_row = 10, verbose = FALSE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod row_label #> 1                          n              4          0         n #> 2                    count.A              2          0         A #> 3                    count.B              1          0         B #> 4                    count.C              1          0         C #> 5           count_fraction.A        2 (50%)          0         A #> 6           count_fraction.B        1 (25%)          0         B #> 7           count_fraction.C        1 (25%)          0         C #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0         A #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0         B #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0         C #> 11                fraction.A    2/4 (50.0%)          0         A #> 12                fraction.B    1/4 (25.0%)          0         B #> 13                fraction.C    1/4 (25.0%)          0         C #> 14                     n_blq              0          0     n_blq a_summary(   c(\"A\", \"B\", \"A\", \"C\"),   .ref_group = c(\"B\", \"A\", \"C\"), .var = \"x\", compare = TRUE, verbose = FALSE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                     row_name formatted_cell indent_mod #> 1                          n              4          0 #> 2                    count.A              2          0 #> 3                    count.B              1          0 #> 4                    count.C              1          0 #> 5           count_fraction.A        2 (50%)          0 #> 6           count_fraction.B        1 (25%)          0 #> 7           count_fraction.C        1 (25%)          0 #> 8  count_fraction_fixed_dp.A      2 (50.0%)          0 #> 9  count_fraction_fixed_dp.B      1 (25.0%)          0 #> 10 count_fraction_fixed_dp.C      1 (25.0%)          0 #> 11                fraction.A    2/4 (50.0%)          0 #> 12                fraction.B    1/4 (25.0%)          0 #> 13                fraction.C    1/4 (25.0%)          0 #> 14                     n_blq              0          0 #> 15               pval_counts         0.9074          0 #>                     row_label #> 1                           n #> 2                           A #> 3                           B #> 4                           C #> 5                           A #> 6                           B #> 7                           C #> 8                           A #> 9                           B #> 10                          C #> 11                          A #> 12                          B #> 13                          C #> 14                      n_blq #> 15 p-value (chi-squared test)  a_summary(c(TRUE, FALSE, FALSE, TRUE, TRUE), .N_row = 10, .N_col = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod      row_label #> 1                       n              5          0              n #> 2                   count              3          0          count #> 3          count_fraction        3 (60%)          0 count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0 count_fraction #> 5                fraction                         0       fraction #> 6                   n_blq              0          0          n_blq a_summary(   c(TRUE, FALSE, FALSE, TRUE, TRUE),   .ref_group = c(TRUE, FALSE), .in_ref_col = TRUE, compare = TRUE ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                  row_name formatted_cell indent_mod                  row_label #> 1                       n              5          0                          n #> 2                   count              3          0                      count #> 3          count_fraction        3 (60%)          0             count_fraction #> 4 count_fraction_fixed_dp      3 (60.0%)          0             count_fraction #> 5                fraction                         0                   fraction #> 6                   n_blq              0          0                      n_blq #> 7             pval_counts                         0 p-value (chi-squared test)  a_summary(rnorm(10), .N_col = 10, .N_row = 20, .var = \"bla\") #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>        row_name    formatted_cell indent_mod                   row_label #> 1             n                10          0                           n #> 2           sum              -4.4          0                         Sum #> 3          mean              -0.4          0                        Mean #> 4            sd               1.1          0                          SD #> 5            se               0.4          0                          SE #> 6       mean_sd        -0.4 (1.1)          0                   Mean (SD) #> 7       mean_se        -0.4 (0.4)          0                   Mean (SE) #> 8       mean_ci     (-1.24, 0.36)          0                 Mean 95% CI #> 9      mean_sei    (-0.79, -0.09)          0               Mean -/+ 1xSE #> 10     mean_sdi     (-1.56, 0.68)          0               Mean -/+ 1xSD #> 11    mean_pval            0.2432          0 Mean p-value (H0: mean = 0) #> 12       median              -0.2          0                      Median #> 13          mad               0.0          0   Median Absolute Deviation #> 14    median_ci     (-1.82, 0.62)          0               Median 95% CI #> 15    quantiles        -1.4 - 0.3          0             25% and 75%-ile #> 16          iqr               1.7          0                         IQR #> 17        range        -2.4 - 1.1          0                   Min - Max #> 18          min              -2.4          0                     Minimum #> 19          max               1.1          0                     Maximum #> 20 median_range -0.2 (-2.4 - 1.1)          0          Median (Min - Max) #> 21           cv            -253.2          0                      CV (%) #> 22    geom_mean                NA          0              Geometric Mean #> 23 geom_mean_ci                NA          0       Geometric Mean 95% CI #> 24      geom_cv                NA          0         CV % Geometric Mean a_summary(rnorm(10, 5, 1), .ref_group = rnorm(20, -5, 1), .var = \"bla\", compare = TRUE) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>        row_name  formatted_cell indent_mod                   row_label #> 1             n              10          0                           n #> 2           sum            48.2          0                         Sum #> 3          mean             4.8          0                        Mean #> 4            sd             1.2          0                          SD #> 5            se             0.4          0                          SE #> 6       mean_sd       4.8 (1.2)          0                   Mean (SD) #> 7       mean_se       4.8 (0.4)          0                   Mean (SE) #> 8       mean_ci    (3.98, 5.66)          0                 Mean 95% CI #> 9      mean_sei    (4.45, 5.19)          0               Mean -/+ 1xSE #> 10     mean_sdi    (3.65, 6.00)          0               Mean -/+ 1xSD #> 11    mean_pval         <0.0001          0 Mean p-value (H0: mean = 0) #> 12       median             4.7          0                      Median #> 13          mad             0.0          0   Median Absolute Deviation #> 14    median_ci    (3.37, 5.63)          0               Median 95% CI #> 15    quantiles       4.1 - 5.5          0             25% and 75%-ile #> 16          iqr             1.5          0                         IQR #> 17        range       3.1 - 7.1          0                   Min - Max #> 18          min             3.1          0                     Minimum #> 19          max             7.1          0                     Maximum #> 20 median_range 4.7 (3.1 - 7.1)          0          Median (Min - Max) #> 21           cv            24.4          0                      CV (%) #> 22    geom_mean             4.7          0              Geometric Mean #> 23 geom_mean_ci    (3.93, 5.60)          0       Geometric Mean 95% CI #> 24      geom_cv            25.2          0         CV % Geometric Mean #> 25         pval         <0.0001          0            p-value (t-test)"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze numeric variables in columns — analyze_vars_in_cols","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout-creating function analyze_vars_in_cols() creates layout element generate column-wise analysis table. function sets analysis methods column labels wrapper rtables::analyze_colvars(). designed principally PK tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"analyze_vars_in_cols(   lyt,   vars,   ...,   .stats = c(\"n\", \"mean\", \"sd\", \"se\", \"cv\", \"geom_cv\"),   .labels = c(n = \"n\", mean = \"Mean\", sd = \"SD\", se = \"SE\", cv = \"CV (%)\", geom_cv =     \"CV % Geometric Mean\"),   row_labels = NULL,   do_summarize_row_groups = FALSE,   split_col_vars = TRUE,   imp_rule = NULL,   avalcat_var = \"AVALCAT1\",   cache = FALSE,   .indent_mods = NULL,   na_str = default_na_str(),   nested = TRUE,   .formats = NULL,   .aligns = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . ... additional arguments lower level functions. .stats (character) statistics select table. .labels (named character) labels statistics (without indent). row_labels (character) function works columns space, usually .labels character vector applies column space. can change row labels defining parameter named character vector names corresponding split values. defaults NULL contains one string, duplicate row label. do_summarize_row_groups (flag) defaults FALSE applies analysis current label rows. wrapper rtables::summarize_row_groups() can accept labelstr define row labels. behavior supported never need overload row labels. split_col_vars (flag) defaults TRUE puts analysis results onto columns. option allows add multiple instances functions, also nested fashion, without adding splits. split must happen one time single layout. imp_rule (string NULL) imputation rule setting. Defaults NULL imputation rule. Can also \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. order use imputation rule, avalcat_var argument must specified. See imputation_rule() details imputation. avalcat_var (string) imp_rule NULL, name variable indicates whether row data corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable must present data match variable used calculate n_blq statistic (included .stats). cache (flag) whether store computed values temporary caching environment. speed calculations large tables, set FALSE rtable layout used multiple tables different data. Defaults FALSE. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"experimental implementation rtables::summarize_row_groups() rtables::analyze_colvars() may subjected changes rtables extends support complex analysis pipelines column space. encourage users read examples carefully file issues different use cases. function, labelstr behaves atypically. labelstr = NULL (default), row labels assigned automatically split values do_summarize_row_groups = FALSE (default), group label do_summarize_row_groups = TRUE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/analyze_vars_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze numeric variables in columns — analyze_vars_in_cols","text":"","code":"library(dplyr)  # Data preparation adpp <- tern_ex_adpp %>% h_pkparam_sort()  lyt <- basic_table() %>%   split_rows_by(var = \"STRATA1\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>% # Removes duplicated labels   analyze_vars_in_cols(vars = \"AGE\") result <- build_table(lyt = lyt, df = adpp) result #> STRATA1                                                          #>   SEX      n    Mean    SD    SE    CV (%)   CV % Geometric Mean #> ———————————————————————————————————————————————————————————————— #> A                                                                #>   F       81    38.8   5.4    0.6    13.8           14.3         #>   M       81    38.9   5.9    0.7    15.1           14.9         #> B                                                                #>   F       90    36.0   6.4    0.7    17.7           17.9         #>   M       81    36.4   6.5    0.7    17.9           17.8         #> C                                                                #>   F       117   34.1   6.2    0.6    18.2           18.3         #>   M       72    33.2   11.5   1.4    34.6           31.6          # By selecting just some statistics and ad-hoc labels lyt <- basic_table() %>%   split_rows_by(var = \"ARM\", label_pos = \"topleft\") %>%   split_rows_by(     var = \"SEX\",     label_pos = \"topleft\",     child_labels = \"hidden\",     split_fun = drop_split_levels   ) %>%   analyze_vars_in_cols(     vars = \"AGE\",     .stats = c(\"n\", \"cv\", \"geom_mean\"),     .labels = c(       n = \"aN\",       cv = \"aCV\",       geom_mean = \"aGeomMean\"     )   ) result <- build_table(lyt = lyt, df = adpp) result #> ARM                                     #>   SEX            aN    aCV    aGeomMean #> ——————————————————————————————————————— #> A: Drug X                               #> B: Placebo                              #> C: Combination                          #>   F              288   17.6     35.5    #>   M              234   23.4     35.3     # Changing row labels lyt <- basic_table() %>%   analyze_vars_in_cols(     vars = \"AGE\",     row_labels = \"some custom label\"   ) result <- build_table(lyt, df = adpp) result #>                      n    Mean   SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————————— #> some custom label   522   36.1   7.4   0.3    20.4           20.6          # Pharmacokinetic parameters lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\",     child_labels = \"hidden\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\"   ) result <- build_table(lyt, df = adpp) result #> PK Parameter   n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4          # Multiple calls (summarize label and analyze underneath) lyt <- basic_table() %>%   split_rows_by(     var = \"TLG_DISPLAY\",     split_label = \"PK Parameter\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     do_summarize_row_groups = TRUE # does a summarize level   ) %>%   split_rows_by(\"SEX\",     child_labels = \"hidden\",     label_pos = \"topleft\"   ) %>%   analyze_vars_in_cols(     vars = \"AVAL\",     split_col_vars = FALSE # avoids re-splitting the columns   ) result <- build_table(lyt, df = adpp) result #> PK Parameter                                                          #>   SEX          n    Mean     SD    SE    CV (%)   CV % Geometric Mean #> ————————————————————————————————————————————————————————————————————— #> Cmax           58   29.7    5.6    0.7    19.0           19.3         #>   F            32   30.1    6.1    1.1    20.4           21.0         #>   M            26   29.2    5.0    1.0    17.2           17.2         #> AUCinf obs     58   207.5   34.9   4.6    16.8           17.3         #>   F            32   209.5   43.3   7.7    20.7           21.6         #>   M            26   205.0   20.9   4.1    10.2           10.4         #> CL obs         58    5.1    1.0    0.1    20.6           22.7         #>   F            32    5.1    1.1    0.2    20.8           23.2         #>   M            26    5.1    1.1    0.2    20.7           22.5         #> Ae             58    1.5    0.3    0.0    21.3           24.1         #>   F            32    1.5    0.3    0.1    19.3           20.8         #>   M            26    1.5    0.4    0.1    23.9           27.9         #> Fe             58   15.7    3.6    0.5    22.7           24.0         #>   F            32   16.3    3.4    0.6    20.9           22.3         #>   M            26   15.0    3.7    0.7    24.7           25.6         #> CLR            58    0.0    0.0    0.0    19.9           22.2         #>   F            32    0.0    0.0    0.0    20.5           24.8         #>   M            26    0.0    0.0    0.0    19.5           18.9         #> Rmax           58    9.6    2.0    0.3    21.1           21.6         #>   F            32    9.6    2.2    0.4    22.4           23.5         #>   M            26    9.6    1.9    0.4    19.7           19.5         #> Tonset         58    3.0    0.7    0.1    22.4           23.3         #>   F            32    3.0    0.7    0.1    24.7           25.9         #>   M            26    3.0    0.6    0.1    19.8           20.0         #> RENALCLD       58    0.0    0.0    0.0    19.0           19.4         #>   F            32    0.0    0.0    0.0    19.6           20.4         #>   M            26    0.0    0.0    0.0    18.0           17.6"},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add variable labels to top left corner in table — append_varlabels","title":"Add variable labels to top left corner in table — append_varlabels","text":"Helper layout-creating function append variable labels given variables vector given dataset top left corner. variable label found variable name used instead. Multiple variable labels concatenated slashes.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"append_varlabels(lyt, df, vars, indent = 0L)"},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add variable labels to top left corner in table — append_varlabels","text":"lyt (PreDataTableLayouts) layout analyses added . df (data.frame) data set containing analysis variables. vars (character) variable names labels looked df. indent (integer(1)) non-negative number nested indent space, default 0L means indent. 1L means two spaces indent, 2L means four spaces indent .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add variable labels to top left corner in table — append_varlabels","text":"modified layout new variable label(s) added top-left material.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Add variable labels to top left corner in table — append_varlabels","text":"optimal implementation course, since using data set layout creation. mature rtables implementation also improved necessary anymore.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/append_varlabels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add variable labels to top left corner in table — append_varlabels","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   split_rows_by(\"SEX\") %>%   append_varlabels(DM, \"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, \"AGE\", indent = 1) build_table(lyt, DM) #> SEX                   A: Drug X          B: Placebo       C: Combination  #>   Age                  (N=121)            (N=106)            (N=129)      #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA         lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   analyze(\"AGE\", afun = mean) %>%   append_varlabels(DM, c(\"SEX\", \"AGE\")) build_table(lyt, DM) #> SEX / Age             A: Drug X          B: Placebo       C: Combination  #> ————————————————————————————————————————————————————————————————————————— #> F                                                                         #>   mean             33.7142857142857   33.8392857142857   34.8852459016393 #> M                                                                         #>   mean             36.5490196078431         32.1         34.2794117647059 #> U                                                                         #>   mean                    NA                 NA                 NA        #> UNDIFFERENTIATED                                                          #>   mean                    NA                 NA                 NA"},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply automatic formatting — apply_auto_formatting","title":"Apply automatic formatting — apply_auto_formatting","text":"Checks listed formats .formats \"auto\", replaces \"auto\" correct implementation format_auto given statistics, data, variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply automatic formatting — apply_auto_formatting","text":"","code":"apply_auto_formatting(.formats, x_stats, .df_row, .var)"},{"path":"https://insightsengineering.github.io/tern/reference/apply_auto_formatting.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply automatic formatting — apply_auto_formatting","text":".formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. x_stats (named list) named list statistics element corresponds element .formats, matching names. .df_row (data.frame) data frame across columns given row split. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard arguments — argument_convention","title":"Standard arguments — argument_convention","text":"documentation function lists arguments tern used repeatedly express analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard arguments — argument_convention","text":"... additional arguments lower level functions. .aligns (character NULL) alignment table contents (including labels). NULL, \"center\" applied. See formatters::list_valid_aligns() list currently supported alignments. .all_col_counts (integer) vector value represents global count column. Values taken alt_counts_df specified (see rtables::build_table()). .df_row (data.frame) data frame across columns given row split. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. .ref_group (data.frame vector) data corresponding reference group. .spl_context (data.frame) gives information ancestor split states passed rtables. .stats (character) statistics select table. .var (string) single variable name passed rtables requested statistics function. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. col_by (factor) defining column groups. conf_level (proportion) confidence level interval. data (data.frame) dataset containing variables summarize. df (data.frame) data set containing analysis variables. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. id (string) subject variable name. is_event (flag)TRUE event, FALSE time event censored. label_all (string) label total population analysis. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. lyt (PreDataTableLayouts) layout analyses added . method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. na.rm (flag) whether NA values removed x prior analysis. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. prune_zero_rows (flag) whether prune zero rows. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. rsp (logical) vector indicating whether subject responder . show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. tte (numeric) vector time--event duration values. var_labels (character) variable labels. variables (named list string) list additional analysis variables. vars (character) variable names primary analysis variable iterated . var (string) single variable name primary analysis variable. x (numeric) vector numbers want analyze. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/argument_convention.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Standard arguments — argument_convention","text":"Although function just returns NULL two uses, tern users provides documentation arguments commonly consistently used framework. developer adds single reference point import roxygen argument description : @inheritParams argument_convention","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Arrange multiple grobs — arrange_grobs","title":"Arrange multiple grobs — arrange_grobs","text":"Arrange grobs new grob n * m (rows * cols) layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"arrange_grobs(   ...,   grobs = list(...),   ncol = NULL,   nrow = NULL,   padding_ht = grid::unit(2, \"line\"),   padding_wt = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Arrange multiple grobs — arrange_grobs","text":"... grobs. grobs (list grob) list grobs. ncol (integer(1)) number columns layout. nrow (integer(1)) number rows layout. padding_ht (grid::unit) unit length 1, vertical space grob. padding_wt (grid::unit) unit length 1, horizontal space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Arrange multiple grobs — arrange_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/arrange_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Arrange multiple grobs — arrange_grobs","text":"","code":"library(grid)  # \\donttest{ num <- lapply(1:9, textGrob) grid::grid.newpage() grid.draw(arrange_grobs(grobs = num, ncol = 2)) #> Warning: `arrange_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  showViewport()   g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, nrow = 2))  showViewport()   grid::grid.newpage() grid.draw(arrange_grobs(g1, g2, g3, ncol = 3))   grid::grid.newpage() grid::pushViewport(grid::viewport(layout = grid::grid.layout(1, 2))) vp1 <- grid::viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(arrange_grobs(g1, g2, g3, ncol = 2, vp = vp1))  showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert to rtable — as.rtable","title":"Convert to rtable — as.rtable","text":"new generic function convert objects rtable tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert to rtable — as.rtable","text":"","code":"as.rtable(x, ...)  # S3 method for class 'data.frame' as.rtable(x, format = \"xx.xx\", ...)"},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert to rtable — as.rtable","text":"x (data.frame) object converted rtable. ... additional arguments methods. format (string function) format used columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert to rtable — as.rtable","text":"rtables table object. Note concrete class depend method used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Convert to rtable — as.rtable","text":".rtable(data.frame): Method converting data.frame contains numeric columns rtable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as.rtable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert to rtable — as.rtable","text":"","code":"x <- data.frame(   a = 1:10,   b = rnorm(10) ) as.rtable(x) #>        a       b   #> —————————————————— #> 1    1.00    0.07  #> 2    2.00    -0.64 #> 3    3.00    -0.05 #> 4    4.00    -0.25 #> 5    5.00    0.44  #> 6    6.00    2.76  #> 7    7.00    0.05  #> 8    8.00    0.58  #> 9    9.00    0.12  #> 10   10.00   -1.91"},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of a vector to a factor — as_factor_keep_attributes","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"Converts x factor keeps attributes. Warns appropriately user can decide whether prefer converting factor manually (e.g. full control factor levels).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"","code":"as_factor_keep_attributes(   x,   x_name = deparse(substitute(x)),   na_level = \"<Missing>\",   verbose = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"x (vector) object convert. x_name (string) name x. na_level (string) explicit missing level used converting character vector. verbose (flag) defaults TRUE. prints warnings messages.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/as_factor_keep_attributes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of a vector to a factor — as_factor_keep_attributes","text":"factor attributes (except class) x. modify x already factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional assertions to use with checkmate — assertions","title":"Additional assertions to use with checkmate — assertions","text":"Additional assertion functions can used together checkmate package.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Additional assertions to use with checkmate — assertions","text":"","code":"assert_list_of_variables(x, .var.name = checkmate::vname(x), add = NULL)  assert_df_with_variables(   df,   variables,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_valid_factor(   x,   min.levels = 1,   max.levels = NULL,   null.ok = TRUE,   any.missing = TRUE,   n.levels = NULL,   len = NULL,   .var.name = checkmate::vname(x),   add = NULL )  assert_df_with_factors(   df,   variables,   min.levels = 1,   max.levels = NULL,   any.missing = TRUE,   na_level = NULL,   .var.name = checkmate::vname(df),   add = NULL )  assert_proportion_value(x, include_boundaries = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Additional assertions to use with checkmate — assertions","text":"x () object test. .var.name [character(1)] Name checked object print assertions. Defaults heuristic implemented vname. add [AssertCollection] Collection store assertion messages. See AssertCollection. df (data.frame) data set test. variables (named list character) list variables test. na_level (string) string using represent NA missing data. NA values please consider using directly .na() similar approaches. min.levels [integer(1)] Minimum number factor levels. Default NULL (check). max.levels [integer(1)] Maximum number factor levels. Default NULL (check). null.ok [logical(1)] set TRUE, x may also NULL. case type check x performed, additional checks disabled. .missing [logical(1)] vectors missing values allowed? Default TRUE. n.levels [integer(1)] Exact number factor levels. Default NULL (check). len [integer(1)] Exact expected length x. include_boundaries (flag) whether include boundaries testing proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional assertions to use with checkmate — assertions","text":"Nothing assertion passes, otherwise prints error message.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/assertions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Additional assertions to use with checkmate — assertions","text":"assert_list_of_variables(): Checks whether x valid list variable names. NULL elements list x dropped Filter(Negate(.null), x). assert_df_with_variables(): Check whether df data frame analysis variables. Please notice produces error variables present data.frame opposite required. assert_valid_factor(): Check whether x valid factor (.e. levels empty string levels). Note NULL NA elements allowed. assert_df_with_factors(): Check whether df data frame analysis variables factors. Note creation NA direct call factor() trim NA levels vector list . assert_proportion_value(): Check whether x proportion: number 0 1.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for bins in percent — bins_percent_labels","title":"Labels for bins in percent — bins_percent_labels","text":"creates labels quantile based bins percent. assumes right-closed intervals produced cut_quantile_bins().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for bins in percent — bins_percent_labels","text":"","code":"bins_percent_labels(probs, digits = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for bins in percent — bins_percent_labels","text":"probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. digits (integer(1)) number decimal places round percent numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/bins_percent_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for bins in percent — bins_percent_labels","text":"character vector labels format [0%,20%], (20%,50%], etc.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add row total to labels — c_label_n","title":"Content row function to add row total to labels — c_label_n","text":"takes label latest row split level adds row total df parentheses. function differs c_label_n_alt() taking row counts df rather alt_counts_df, used add_rowcounts() alt_counts set FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add row total to labels — c_label_n","text":"","code":"c_label_n(df, labelstr, .N_row)"},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add row total to labels — c_label_n","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add row total to labels — c_label_n","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Content row function to add row total to labels — c_label_n","text":"important use df rather .N_row implementation, former already split columns refer first column data .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":null,"dir":"Reference","previous_headings":"","what":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"takes label latest row split level adds row total alt_counts_df parentheses. function differs c_label_n() taking row counts alt_counts_df rather df, used add_rowcounts() alt_counts set TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"","code":"c_label_n_alt(df, labelstr, .alt_df_row)"},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/c_label_n_alt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Content row function to add alt_counts_df row total to labels — c_label_n_alt","text":"list formatted rtables::CellValue() row count value correct label.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Constructor for content functions given a data frame with flag input — cfun_by_flag","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"can useful tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"","code":"cfun_by_flag(analysis_var, flag_var, format = \"xx\", .indent_mods = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"analysis_var (string) variable name column containing values returned content function. flag_var (string) variable name logical column identifying row returned. format (string)rtables format use.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cfun_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Constructor for content functions given a data frame with flag input — cfun_by_flag","text":"content function gives df$analysis_var row identified .df_row$flag given format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Check proportion difference arguments — check_diff_prop_ci","title":"Check proportion difference arguments — check_diff_prop_ci","text":"Verifies /convert arguments valid values used estimation difference responder proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check proportion difference arguments — check_diff_prop_ci","text":"","code":"check_diff_prop_ci(rsp, grp, strata = NULL, conf_level, correct = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/check_diff_prop_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check proportion difference arguments — check_diff_prop_ci","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). strata (factor) variable one level per stratum length rsp. conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Check element dimension — check_same_n","title":"Check element dimension — check_same_n","text":"Checks elements ... dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check element dimension — check_same_n","text":"","code":"check_same_n(..., omit_null = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check element dimension — check_same_n","text":"... (data.frame vector) data frames vectors. omit_null (flag) whether NULL elements ... omitted check.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/check_same_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check element dimension — check_same_n","text":"logical value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":null,"dir":"Reference","previous_headings":"","what":"Class for CombinationFunction — combination_function","title":"Class for CombinationFunction — combination_function","text":"CombinationFunction S4 class extends standard functions. special functions can combined negated logical operators.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Class for CombinationFunction — combination_function","text":"","code":"# S4 method for class 'CombinationFunction,CombinationFunction' e1 & e2  # S4 method for class 'CombinationFunction,CombinationFunction' e1 | e2  # S4 method for class 'CombinationFunction' !x"},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Class for CombinationFunction — combination_function","text":"e1 (CombinationFunction) left hand side logical operator. e2 (CombinationFunction) right hand side logical operator. x (CombinationFunction) function negated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Class for CombinationFunction — combination_function","text":"logical value indicating whether left hand side equation equals right hand side.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Class for CombinationFunction — combination_function","text":"e1 & e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. e1 | e2: Logical \"\" combination CombinationFunction functions. resulting object class, evaluates two argument functions. result \"\" two individual results. `!`(CombinationFunction): Logical negation CombinationFunction functions. resulting object class, evaluates original function. result opposite results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combination_function.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Class for CombinationFunction — combination_function","text":"","code":"higher <- function(a) {   force(a)   CombinationFunction(     function(x) {       x > a     }   ) }  lower <- function(b) {   force(b)   CombinationFunction(     function(x) {       x < b     }   ) }  c1 <- higher(5) c2 <- lower(10) c3 <- higher(5) & lower(10) c3(7) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine counts — combine_counts","title":"Combine counts — combine_counts","text":"Simplifies estimation column counts, especially group combination required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine counts — combine_counts","text":"","code":"combine_counts(fct, groups_list = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine counts — combine_counts","text":"fct (factor) variable levels needs grouped. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine counts — combine_counts","text":"vector column counts.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/combine_counts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine counts — combine_counts","text":"","code":"ref <- c(\"A: Drug X\", \"B: Placebo\") groups <- combine_groups(fct = DM$ARM, ref = ref)  col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> n                   227                 129       #> Mean (SD)        34.0 (7.2)          34.6 (6.5)   #> Median              33.0                33.0      #> Min - Max       20.0 - 60.0         22.0 - 53.0    ref <- \"A: Drug X\" groups <- combine_groups(fct = DM$ARM, ref = ref) col_counts <- combine_counts(   fct = DM$ARM,   groups_list = groups )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM, col_counts = col_counts) #>              A: Drug X    B: Placebo/C: Combination #>               (N=121)              (N=235)          #> ——————————————————————————————————————————————————— #> n               121                  235            #> Mean (SD)   34.9 (7.8)           33.9 (6.5)         #> Median         33.0                 33.0            #> Min - Max   20.0 - 60.0          21.0 - 55.0"},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Reference and treatment group combination — combine_groups","title":"Reference and treatment group combination — combine_groups","text":"Facilitate re-combination groups divided reference treatment groups; helps arranging groups columns rtables framework teal modules.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reference and treatment group combination — combine_groups","text":"","code":"combine_groups(fct, ref = NULL, collapse = \"/\")"},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reference and treatment group combination — combine_groups","text":"fct (factor) variable levels needs grouped. ref (character) reference level(s). collapse (string) character string separate fct ref.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reference and treatment group combination — combine_groups","text":"list first item ref (reference) second item trt (treatment).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reference and treatment group combination — combine_groups","text":"","code":"groups <- combine_groups(   fct = DM$ARM,   ref = c(\"B: Placebo\") )  basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze_vars(\"AGE\") %>%   build_table(DM) #>             B: Placebo    A: Drug X/C: Combination #>               (N=106)             (N=250)          #> —————————————————————————————————————————————————— #> n               106                 250            #> Mean (SD)   33.0 (6.3)           34.7 (7.1)        #> Median         32.0                 33.0           #> Min - Max   21.0 - 55.0         20.0 - 60.0"},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine factor levels — combine_levels","title":"Combine factor levels — combine_levels","text":"Combine specified old factor Levels single new level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine factor levels — combine_levels","text":"","code":"combine_levels(x, levels, new_level = paste(levels, collapse = \"/\"))"},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine factor levels — combine_levels","text":"x (factor) factor variable. levels (character) level names combined. new_level (string) name new level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine factor levels — combine_levels","text":"factor new levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine factor levels — combine_levels","text":"","code":"x <- factor(letters[1:5], levels = letters[5:1]) combine_levels(x, levels = c(\"a\", \"b\")) #> [1] a/b a/b c   d   e   #> Levels: e d c a/b  combine_levels(x, c(\"e\", \"b\")) #> [1] a   e/b c   d   e/b #> Levels: e/b d c a"},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Element-wise combination of two vectors — combine_vectors","title":"Element-wise combination of two vectors — combine_vectors","text":"Element-wise combination two vectors","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(x, y)"},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Element-wise combination of two vectors — combine_vectors","text":"x (vector) first vector combine. y (vector) second vector combine.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Element-wise combination of two vectors — combine_vectors","text":"list element combines corresponding elements x y.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/combine_vectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Element-wise combination of two vectors — combine_vectors","text":"","code":"combine_vectors(1:3, 4:6) #> [[1]] #> [1] 1 4 #>  #> [[2]] #> [1] 2 5 #>  #> [[3]] #> [1] 3 6 #>"},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare variables between groups — compare_variables","title":"Compare variables between groups — compare_variables","text":"analyze function compare_vars() creates layout element summarize compare one variables, using S3 generic function s_summary() calculate list summary statistics. list available statistics numeric variables can viewed running get_stats(\"analyze_vars_numeric\", add_pval = TRUE) non-numeric variables running get_stats(\"analyze_vars_counts\", add_pval = TRUE). Use .stats parameter specify statistics include output summary table. Prior using function table layout must use rtables::split_cols_by() create column split variable used comparisons, specify reference group via ref_group parameter. Comparisons can performed group (column) specified reference group including p-value statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare variables between groups — compare_variables","text":"","code":"compare_vars(   lyt,   vars,   var_labels = vars,   na_str = default_na_str(),   nested = TRUE,   ...,   na.rm = TRUE,   show_labels = \"default\",   table_names = vars,   section_div = NA_character_,   .stats = c(\"n\", \"mean_sd\", \"count_fraction\", \"pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'numeric' s_compare(x, .ref_group, .in_ref_col, ...)  # S3 method for class 'factor' s_compare(x, .ref_group, .in_ref_col, denom = \"n\", na.rm = TRUE, ...)  # S3 method for class 'character' s_compare(   x,   .ref_group,   .in_ref_col,   denom = \"n\",   na.rm = TRUE,   .var,   verbose = TRUE,   ... )  # S3 method for class 'logical' s_compare(x, .ref_group, .in_ref_col, na.rm = TRUE, denom = \"n\", ...)"},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare variables between groups — compare_variables","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... arguments passed s_compare(). na.rm (flag) whether NA values removed x prior analysis. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. section_div (string) string repeated section divider group defined split instruction, NA_character_ (default) section divider. .stats (character) statistics select table. Options numeric variables : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv', 'pval' Options non-numeric variables : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction', 'n_blq', 'pval_counts' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. x (numeric) vector numbers want analyze. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. denom (string) choice denominator factor proportions, can n (number values row column intersection). .var (string) single variable name passed rtables requested statistics function. verbose (flag) whether warnings messages printed. Mainly used print information factor casting. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compare variables between groups — compare_variables","text":"compare_vars() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_compare() table layout. s_compare() returns output s_summary() comparisons versus reference group form p-values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Compare variables between groups — compare_variables","text":"compare_vars(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_compare(): S3 generic function produce comparison summary. s_compare(numeric): Method numeric class. uses standard t-test calculate p-value. s_compare(factor): Method factor class. uses chi-squared test calculate p-value. s_compare(character): Method character class. makes automatic conversion factor (warning) forwards method factors. s_compare(logical): Method logical class. chi-squared test used. missing values removed, counted FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Compare variables between groups — compare_variables","text":"factor variables, denom factor proportions can n since purpose compare proportions columns, therefore row-based proportion make sense. Proportion based N_col difficult since use counts chi-squared test statistic, therefore missing values accounted explicit factor levels. factor variables contain NA, NA values excluded default. include NA values set na.rm = FALSE missing values displayed NA level. Alternatively, explicit factor level can defined NA values pre-processing via df_explicit_na() - default na_level (\"<Missing>\") also excluded na.rm set TRUE. character variables, automatic conversion factor guarantee table generated correctly. particular sparse tables likely can fail. Therefore always better manually convert character variables factors pre-processing. compare_vars(), column split must define reference group via ref_group comparison well defined.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/compare_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compare variables between groups — compare_variables","text":"","code":"# `compare_vars()` in `rtables` pipelines  ## Default output within a `rtables` pipeline. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM B\") %>%   compare_vars(c(\"AGE\", \"SEX\")) build_table(lyt, tern_ex_adsl) #>                                  ARM A        ARM B        ARM C    #> ——————————————————————————————————————————————————————————————————— #> AGE                                                                 #>   n                                69           73           58     #>   Mean (SD)                    34.1 (6.8)   35.8 (7.1)   36.1 (7.4) #>   p-value (t-test)               0.1446                    0.8212   #> SEX                                                                 #>   n                                69           73           58     #>   F                            38 (55.1%)   40 (54.8%)   32 (55.2%) #>   M                            31 (44.9%)   33 (45.2%)   26 (44.8%) #>   p-value (chi-squared test)     1.0000                    1.0000    ## Select and format statistics output. lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", ref_group = \"ARM C\") %>%   compare_vars(     vars = \"AGE\",     .stats = c(\"mean_sd\", \"pval\"),     .formats = c(mean_sd = \"xx.x, xx.x\"),     .labels = c(mean_sd = \"Mean, SD\")   ) build_table(lyt, df = tern_ex_adsl) #>                      ARM A       ARM B       ARM C   #> ———————————————————————————————————————————————————— #> Mean, SD           34.1, 6.8   35.8, 7.1   36.1, 7.4 #> p-value (t-test)    0.1176      0.8212                # `s_compare.numeric`  ## Usual case where both this and the reference group vector have more than 1 value. s_compare(rnorm(10, 5, 1), .ref_group = rnorm(5, -5, 1), .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 51.27191  #>  #> $mean #>     mean  #> 5.127191  #>  #> $sd #>       sd  #> 1.226119  #>  #> $se #>       se  #> 0.387733  #>  #> $mean_sd #>     mean       sd  #> 5.127191 1.226119  #>  #> $mean_se #>     mean       se  #> 5.127191 0.387733  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.250078    6.004304  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.739458     5.514924  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.901071     6.353310  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>      p_value  #> 3.353908e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.024369  #>  #> $mad #>           mad  #> -4.440892e-16  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      4.638779      5.862086  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.756763      5.549828  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>       iqr  #> 0.7930643  #>  #> $range #>      min      max  #> 2.725885 7.682557  #>  #> $min #>      min  #> 2.725885  #>  #> $max #>      max  #> 7.682557  #>  #> $median_range #>   median      min      max  #> 5.024369 2.725885 7.682557  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>       cv  #> 23.91406  #>  #> $geom_mean #> geom_mean  #>  4.985435  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.144463    5.997052  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 26.26258  #>  #> $pval #> [1] 2.25779e-08 #>   ## If one group has not more than 1 value, then p-value is not calculated. s_compare(rnorm(10, 5, 1), .ref_group = 1, .in_ref_col = FALSE) #> $n #>  n  #> 10  #>  #> $sum #>      sum  #> 50.71578  #>  #> $mean #>     mean  #> 5.071578  #>  #> $sd #>       sd  #> 1.105832  #>  #> $se #>        se  #> 0.3496948  #>  #> $mean_sd #>     mean       sd  #> 5.071578 1.105832  #>  #> $mean_se #>      mean        se  #> 5.0715780 0.3496948  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.280513    5.862643  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>     4.721883     5.421273  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>     3.965746     6.177410  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #>      p_value  #> 1.511204e-07  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #>   median  #> 5.260423  #>  #> $mad #> mad  #>   0  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>      3.529264      6.318293  #> attr(,\"conf_level\") #> [1] 0.9785156 #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>      4.024149      6.065057  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #>      iqr  #> 2.040908  #>  #> $range #>      min      max  #> 3.300549 6.337320  #>  #> $min #>      min  #> 3.300549  #>  #> $max #>     max  #> 6.33732  #>  #> $median_range #>   median      min      max  #> 5.260423 3.300549 6.337320  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #>      cv  #> 21.8045  #>  #> $geom_mean #> geom_mean  #>  4.952266  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>    4.181833    5.864639  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #>  geom_cv  #> 23.97201  #>  #> $pval #> character(0) #>   ## Empty numeric does not fail, it returns NA-filled items and no p-value. s_compare(numeric(), .ref_group = numeric(), .in_ref_col = FALSE) #> $n #> n  #> 0  #>  #> $sum #> sum  #>  NA  #>  #> $mean #> mean  #>   NA  #>  #> $sd #> sd  #> NA  #>  #> $se #> se  #> NA  #>  #> $mean_sd #> mean   sd  #>   NA   NA  #>  #> $mean_se #> mean   se  #>   NA   NA  #>  #> $mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Mean 95% CI\" #>  #> $mean_sei #> mean_sei_lwr mean_sei_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSE\" #>  #> $mean_sdi #> mean_sdi_lwr mean_sdi_upr  #>           NA           NA  #> attr(,\"label\") #> [1] \"Mean -/+ 1xSD\" #>  #> $mean_pval #> p_value  #>      NA  #> attr(,\"label\") #> [1] \"Mean p-value (H0: mean = 0)\" #>  #> $median #> median  #>     NA  #>  #> $mad #> mad  #>  NA  #>  #> $median_ci #> median_ci_lwr median_ci_upr  #>            NA            NA  #> attr(,\"conf_level\") #> [1] NA #> attr(,\"label\") #> [1] \"Median 95% CI\" #>  #> $quantiles #> quantile_0.25 quantile_0.75  #>            NA            NA  #> attr(,\"label\") #> [1] \"25% and 75%-ile\" #>  #> $iqr #> iqr  #>  NA  #>  #> $range #> min max  #>  NA  NA  #>  #> $min #> min  #>  NA  #>  #> $max #> max  #>  NA  #>  #> $median_range #> median    min    max  #>     NA     NA     NA  #> attr(,\"label\") #> [1] \"Median (Min - Max)\" #>  #> $cv #> cv  #> NA  #>  #> $geom_mean #> geom_mean  #>       NaN  #>  #> $geom_mean_ci #> mean_ci_lwr mean_ci_upr  #>          NA          NA  #> attr(,\"label\") #> [1] \"Geometric Mean 95% CI\" #>  #> $geom_cv #> geom_cv  #>      NA  #>  #> $pval #> character(0) #>   # `s_compare.factor`  ## Basic usage: x <- factor(c(\"a\", \"a\", \"b\", \"c\", \"a\")) y <- factor(c(\"a\", \"b\", \"c\")) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Management of NA values. x <- explicit_na(factor(c(\"a\", \"a\", \"b\", \"c\", \"a\", NA, NA))) y <- explicit_na(factor(c(\"a\", \"b\", \"c\", NA))) s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x = x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 7 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 2 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0000000 0.4285714 #>  #> $count_fraction$b #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$c #> [1] 1.0000000 0.1428571 #>  #> $count_fraction$`<Missing>` #> [1] 2.0000000 0.2857143 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     7  #>  #> $fraction$b #>   num denom  #>     1     7  #>  #> $fraction$c #>   num denom  #>     1     7  #>  #> $fraction$`<Missing>` #>   num denom  #>     2     7  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.9063036 #>   # `s_compare.character`  ## Basic usage: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\") y <- c(\"a\", \"b\", \"c\") s_compare(x, .ref_group = y, .in_ref_col = FALSE, .var = \"x\", verbose = FALSE) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>   ## Note that missing values handling can make a large difference: x <- c(\"a\", \"a\", \"b\", \"c\", \"a\", NA) y <- c(\"a\", \"b\", \"c\", rep(NA, 20)) s_compare(x,   .ref_group = y, .in_ref_col = FALSE,   .var = \"x\", verbose = FALSE ) #> $n #> [1] 5 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.6 #>  #> $count_fraction$b #> [1] 1.0 0.2 #>  #> $count_fraction$c #> [1] 1.0 0.2 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     5  #>  #> $fraction$b #>   num denom  #>     1     5  #>  #> $fraction$c #>   num denom  #>     1     5  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.7659283 #>  s_compare(x,   .ref_group = y, .in_ref_col = FALSE, .var = \"x\",   na.rm = FALSE, verbose = FALSE ) #> $n #> [1] 6 #>  #> $count #> $count$a #> [1] 3 #>  #> $count$b #> [1] 1 #>  #> $count$c #> [1] 1 #>  #> $count$`<Missing>` #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$a #> [1] 3.0 0.5 #>  #> $count_fraction$b #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$c #> [1] 1.0000000 0.1666667 #>  #> $count_fraction$`<Missing>` #> [1] 1.0000000 0.1666667 #>  #>  #> $fraction #> $fraction$a #>   num denom  #>     3     6  #>  #> $fraction$b #>   num denom  #>     1     6  #>  #> $fraction$c #>   num denom  #>     1     6  #>  #> $fraction$`<Missing>` #>   num denom  #>     1     6  #>  #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.005768471 #>   # `s_compare.logical`  ## Basic usage: x <- c(TRUE, FALSE, TRUE, TRUE) y <- c(FALSE, FALSE, TRUE) s_compare(x, .ref_group = y, .in_ref_col = FALSE) #> $n #> [1] 4 #>  #> $count #> [1] 3 #>  #> $count_fraction #> [1] 3.00 0.75 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.2702894 #>   ## Management of NA values. x <- c(NA, TRUE, FALSE) y <- c(NA, NA, NA, NA, FALSE) s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = TRUE) #> $n #> [1] 2 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.5 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.3864762 #>  s_compare(x, .ref_group = y, .in_ref_col = FALSE, na.rm = FALSE) #> $n #> [1] 3 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0000000 0.3333333 #>  #> $n_blq #> [1] 0 #>  #> $pval_counts #> [1] 0.1675463 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for descriptive statistics — control_analyze_vars","title":"Control function for descriptive statistics — control_analyze_vars","text":"Sets list parameters summaries descriptive statistics. Typically used internally specify details s_summary(). function family mainly used analyze_vars().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for descriptive statistics — control_analyze_vars","text":"","code":"control_analyze_vars(   conf_level = 0.95,   quantiles = c(0.25, 0.75),   quantile_type = 2,   test_mean = 0 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for descriptive statistics — control_analyze_vars","text":"conf_level (proportion) confidence level interval. quantiles (numeric(2)) vector length two specify quantiles calculate. quantile_type (numeric(1)) number 1 9 selecting quantile algorithms used. Default set 2 matches default quantile algorithm SAS proc univariate set QNTLDEF=5. differs R's default. See type stats::quantile(). test_mean (numeric(1)) number test mean null hypothesis calculating p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_analyze_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for descriptive statistics — control_analyze_vars","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Control functions for Kaplan-Meier plot annotation tables — control_annot","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"Auxiliary functions controlling arguments formatting annotation tables can added plots generated via g_km().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot(x = 0.8, y = 0.85, w = 0.32, h = 0.16, fill = TRUE)  control_coxph_annot(   x = 0.29,   y = 0.51,   w = 0.4,   h = 0.125,   fill = TRUE,   ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"x (proportion) x-coordinate center annotation table. y (proportion) y-coordinate center annotation table. w (proportion) relative width annotation table. h (proportion) relative height annotation table. fill (flag character) whether annotation table background fill color. Can also color code use background fill color. TRUE, color code defaults \"#00000020\". ref_lbls (flag) whether reference group explicitly printed labels annotation table. FALSE (default), comparison groups printed table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"control_surv_med_annot(): Control function formatting median survival time annotation table. annotation table can added g_km() setting annot_surv_med=TRUE, can configured using control_surv_med_annot() function setting control_annot_surv_med argument. control_coxph_annot(): Control function formatting Cox-PH annotation table. annotation table can added g_km() setting annot_coxph=TRUE, can configured using control_coxph_annot() function setting control_annot_coxph argument.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control functions for Kaplan-Meier plot annotation tables — control_annot","text":"","code":"control_surv_med_annot() #> $x #> [1] 0.8 #>  #> $y #> [1] 0.85 #>  #> $w #> [1] 0.32 #>  #> $h #> [1] 0.16 #>  #> $fill #> [1] TRUE #>   control_coxph_annot() #> $x #> [1] 0.29 #>  #> $y #> [1] 0.51 #>  #> $w #> [1] 0.4 #>  #> $h #> [1] 0.125 #>  #> $fill #> [1] TRUE #>  #> $ref_lbls #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox-PH model — control_coxph","title":"Control function for Cox-PH model — control_coxph","text":"auxiliary function controlling arguments Cox-PH model, typically used internally specify details Cox-PH model s_coxph_pairwise(). conf_level refers Hazard Ratio estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox-PH model — control_coxph","text":"","code":"control_coxph(   pval_method = c(\"log-rank\", \"wald\", \"likelihood\"),   ties = c(\"efron\", \"breslow\", \"exact\"),   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox-PH model — control_coxph","text":"pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) string specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox-PH model — control_coxph","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for Cox regression — control_coxreg","title":"Control function for Cox regression — control_coxreg","text":"Sets list parameters Cox regression fit. Used internally.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg(   pval_method = c(\"wald\", \"likelihood\"),   ties = c(\"exact\", \"efron\", \"breslow\"),   conf_level = 0.95,   interaction = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for Cox regression — control_coxreg","text":"pval_method (string) method used estimation p.values; wald (default) likelihood. ties (string) among exact (equivalent DISCRETE SAS), efron breslow, see survival::coxph(). Note: equivalent SAS EXACT method R. conf_level (proportion) confidence level interval. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for Cox regression — control_coxreg","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for Cox regression — control_coxreg","text":"","code":"control_coxreg() #> $pval_method #> [1] \"wald\" #>  #> $ties #> [1] \"exact\" #>  #> $conf_level #> [1] 0.95 #>  #> $interaction #> [1] FALSE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for incidence rate — control_incidence_rate","title":"Control function for incidence rate — control_incidence_rate","text":"auxiliary function controlling arguments incidence rate, used internally specify details s_incidence_rate().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(   conf_level = 0.95,   conf_type = c(\"normal\", \"normal_log\", \"exact\", \"byar\"),   input_time_unit = c(\"year\", \"day\", \"week\", \"month\"),   num_pt_year = 100 )"},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for incidence rate — control_incidence_rate","text":"conf_level (proportion) confidence level interval. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric(1)) number patient-years use calculating adverse event rates.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for incidence rate — control_incidence_rate","text":"list components names arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for incidence rate — control_incidence_rate","text":"","code":"control_incidence_rate(0.9, \"exact\", \"month\", 100) #> $conf_level #> [1] 0.9 #>  #> $conf_type #> [1] \"exact\" #>  #> $input_time_unit #> [1] \"month\" #>  #> $num_pt_year #> [1] 100 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for g_lineplot() — control_lineplot_vars","title":"Control function for g_lineplot() — control_lineplot_vars","text":"Default values variables parameter g_lineplot function. variable's default value can overwritten variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars(   x = \"AVISIT\",   y = \"AVAL\",   group_var = \"ARM\",   facet_var = NA,   paramcd = \"PARAMCD\",   y_unit = \"AVALU\",   subject_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for g_lineplot() — control_lineplot_vars","text":"x (string) x-variable name. y (string) y-variable name. group_var (string NA) group variable name. facet_var (string NA) faceting variable name. paramcd (string NA) parameter code variable name. y_unit (string NA) y-axis unit variable name. subject_var (string NA) subject variable name.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for g_lineplot() — control_lineplot_vars","text":"named character vector variable names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_lineplot_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for g_lineplot() — control_lineplot_vars","text":"","code":"control_lineplot_vars() #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"       \"ARM\"   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA  control_lineplot_vars(group_var = NA) #>           x           y   group_var     paramcd      y_unit subject_var  #>    \"AVISIT\"      \"AVAL\"          NA   \"PARAMCD\"     \"AVALU\"   \"USUBJID\"  #>   facet_var  #>          NA"},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for logistic regression model fitting — control_logistic","title":"Control function for logistic regression model fitting — control_logistic","text":"auxiliary function controlling arguments logistic regression models. conf_level refers confidence level used Odds Ratio CIs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"control_logistic(response_definition = \"response\", conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for logistic regression model fitting — control_logistic","text":"response_definition (string) definition event terms response. used fitting logistic regression model left hand side formula. Note evaluated expression result either logical vector factor 2 levels. default just \"response\" original response variable used modified . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for logistic regression model fitting — control_logistic","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for logistic regression model fitting — control_logistic","text":"","code":"# Standard options. control_logistic() #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.95 #>   # Modify confidence level. control_logistic(conf_level = 0.9) #> $response_definition #> [1] \"response\" #>  #> $conf_level #> [1] 0.9 #>   # Use a different response definition. control_logistic(response_definition = \"I(response %in% c('CR', 'PR'))\") #> $response_definition #> [1] \"I(response %in% c('CR', 'PR'))\" #>  #> $conf_level #> [1] 0.95 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for risk difference column — control_riskdiff","title":"Control function for risk difference column — control_riskdiff","text":"Sets list parameters use generating risk (proportion) difference column. Used input riskdiff parameter tabulate_rsp_subgroups() tabulate_survival_subgroups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff(   arm_x = NULL,   arm_y = NULL,   format = \"xx.x (xx.x - xx.x)\",   col_label = \"Risk Difference (%) (95% CI)\",   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for risk difference column — control_riskdiff","text":"arm_x (string) name reference arm use risk difference calculations. arm_y (character) names one arms compare reference arm risk difference calculations. new column added value arm_y. format (string function) format label (string) formatting function apply risk difference statistic. See 3d string options formatters::list_valid_format_labels() possible format strings. Defaults \"xx.x (xx.x - xx.x)\". col_label (character) labels use rendering risk difference column within table. one comparison arm specified arm_y, default labels specify two arms compared (reference arm vs. comparison arm). pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for risk difference column — control_riskdiff","text":"list items names corresponding arguments.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/control_riskdiff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for risk difference column — control_riskdiff","text":"","code":"control_riskdiff() #> $arm_x #> NULL #>  #> $arm_y #> NULL #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>  control_riskdiff(arm_x = \"ARM A\", arm_y = \"ARM B\") #> $arm_x #> [1] \"ARM A\" #>  #> $arm_y #> [1] \"ARM B\" #>  #> $format #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $col_label #> [1] \"Risk Difference (%) (95% CI)\" #>  #> $pct #> [1] TRUE #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"auxiliary function controlling arguments STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"control_step(   biomarker = NULL,   use_percentile = TRUE,   bandwidth,   degree = 0L,   num_points = 39L )"},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"biomarker (numeric NULL) optional provision numeric biomarker variable, used infer bandwidth, see . use_percentile (flag) TRUE, running windows created according quantiles rather actual values, .e. bandwidth refers percentage data covered window. Suggest TRUE biomarker variable uniformly distributed. bandwidth (numeric(1) NULL) indicating bandwidth window. Depending argument use_percentile, can either length actual-value windows real biomarker scale, percentage windows. use_percentile = TRUE, number 0 1. NULL, treat bandwidth infinity, means one global model fitted. default, 0.25 used percentage windows one quarter range biomarker variable actual-value windows. degree (integer(1)) degree polynomial function biomarker interaction term treatment arm fitted window. 0 (default), biomarker variable included model fitted biomarker window. num_points (integer(1)) number points hazard ratios estimated. smallest number 2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"list components names arguments, except biomarker just used calculate bandwidth case actual biomarker windows requested.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Control function for subgroup treatment effect pattern (STEP) calculations — control_step","text":"","code":"# Provide biomarker values and request actual values to be used, # so that bandwidth is chosen from range. control_step(biomarker = 1:10, use_percentile = FALSE) #> $use_percentile #> [1] FALSE #>  #> $bandwidth #> [1] 2.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 39 #>   # Use a global model with quadratic biomarker interaction term. control_step(bandwidth = NULL, degree = 2) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> NULL #>  #> $degree #> [1] 2 #>  #> $num_points #> [1] 39 #>   # Reduce number of points to be used. control_step(num_points = 10) #> $use_percentile #> [1] TRUE #>  #> $bandwidth #> [1] 0.25 #>  #> $degree #> [1] 0 #>  #> $num_points #> [1] 10 #>"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for survival time — control_surv_time","title":"Control function for survfit models for survival time — control_surv_time","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_time(). conf_level refers survival time estimation.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for survival time — control_surv_time","text":"","code":"control_surv_time(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\"),   quantiles = c(0.25, 0.75) )"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for survival time — control_surv_time","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. quantiles (numeric(2)) vector length two specifying quantiles survival time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for survival time — control_surv_time","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"auxiliary function controlling arguments survfit model, typically used internally specify details survfit model s_surv_timepoint(). conf_level refers patient risk estimation time point.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"","code":"control_surv_timepoint(   conf_level = 0.95,   conf_type = c(\"plain\", \"log\", \"log-log\") )"},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"conf_level (proportion) confidence level interval. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/control_surv_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Control function for survfit models for patients' survival rate at time points — control_surv_timepoint","text":"list components names arguments.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Cumulative counts of numeric variable by thresholds — count_cumulative","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"analyze function count_cumulative() creates layout element calculate cumulative counts values numeric variable less , less equal , greater , greater equal user-specified threshold values. function analyzes numeric variable vars threshold values supplied thresholds argument numeric vector. Whether counts include threshold values, whether count values lower higher threshold values can set via include_eq lower_tail parameters, respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"count_cumulative(   lyt,   vars,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   ... )  a_count_cumulative(   x,   thresholds,   lower_tail = TRUE,   include_eq = TRUE,   .N_col,   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) vector cutoff values counts. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_cumulative() table layout. s_count_cumulative() returns named list count_fractions: list thresholds value component, component containing vector count fraction. a_count_cumulative() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"count_cumulative(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_cumulative(): Statistics function produces named list given numeric vector thresholds. a_count_cumulative(): Formatted analysis function used afun count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cumulative counts of numeric variable by thresholds — count_cumulative","text":"","code":"basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_cumulative(     vars = \"AGE\",     thresholds = c(40, 60)   ) %>%   build_table(tern_ex_adsl) #>           A: Drug X    B: Placebo   C: Combination #>             (N=69)       (N=73)         (N=58)     #> —————————————————————————————————————————————————— #> AGE                                                #>   <= 40   52 (75.4%)   58 (79.5%)     41 (70.7%)   #>   <= 60   69 (100%)    73 (100%)      58 (100%)"},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients with missed doses by thresholds — count_missed_doses","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"analyze function creates layout element calculate cumulative counts patients number missed doses least equal user-specified threshold values. function analyzes numeric variable vars, variable numbers missed doses, threshold values supplied thresholds argument numeric vector. function assumes every row given data frame corresponds unique patient.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"count_missed_doses(   lyt,   vars,   thresholds,   var_labels = vars,   show_labels = \"visible\",   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_nonmissing(x)  s_count_missed_doses(x, thresholds, .N_col)  a_count_missed_doses(x, thresholds, .N_col)"},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . thresholds (numeric) minimum number missed doses patients . var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_missed_doses() table layout. s_count_nonmissing() returns statistic n count non-missing values x. s_count_missed_doses() returns statistics n count_fraction one element threshold. a_count_missed_doses() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"count_missed_doses(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_nonmissing(): Statistics function count non-missing values. s_count_missed_doses(): Statistics function count patients missed doses. a_count_missed_doses(): Formatted analysis function used afun count_missed_doses().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_missed_doses.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients with missed doses by thresholds — count_missed_doses","text":"","code":"library(dplyr)  anl <- tern_ex_adsl %>%   distinct(STUDYID, USUBJID, ARM) %>%   mutate(     PARAMCD = \"TNDOSMIS\",     PARAM = \"Total number of missed doses during study\",     AVAL = sample(0:20, size = nrow(tern_ex_adsl), replace = TRUE),     AVALC = \"\"   )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_missed_doses(\"AVAL\", thresholds = c(1, 5, 10, 15), var_labels = \"Missed Doses\") %>%   build_table(anl, alt_counts_df = tern_ex_adsl) #>                              A: Drug X    B: Placebo   C: Combination #>                                (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————— #> Missed Doses                                                          #>   n                              69           73             58       #>   At least 1 missed dose     69 (100%)    69 (94.5%)     55 (94.8%)   #>   At least 5 missed doses    57 (82.6%)   55 (75.3%)     50 (86.2%)   #>   At least 10 missed doses    40 (58%)    40 (54.8%)     32 (55.2%)   #>   At least 15 missed doses   26 (37.7%)   25 (34.2%)     13 (22.4%)"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences — count_occurrences","title":"Count occurrences — count_occurrences","text":"analyze function count_occurrences() creates layout element calculate occurrence counts patients. function analyzes variable(s) supplied vars returns table occurrence counts unique value (level) variable(s). variable (variables) must non-numeric. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences value recorded patient, value counted . summarize function summarize_occurrences() performs function count_occurrences() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences — count_occurrences","text":"","code":"count_occurrences(   lyt,   vars,   id = \"USUBJID\",   drop = TRUE,   var_labels = vars,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  summarize_occurrences(   lyt,   var,   id = \"USUBJID\",   drop = TRUE,   riskdiff = FALSE,   na_str = default_na_str(),   ...,   .stats = \"count_fraction_fixed_dp\",   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences(   df,   denom = c(\"N_col\", \"n\"),   .N_col,   .df_row,   drop = TRUE,   .var = \"MHDECOD\",   id = \"USUBJID\" )  a_count_occurrences(   df,   labelstr = \"\",   id = \"USUBJID\",   denom = c(\"N_col\", \"n\"),   drop = TRUE,   .N_col,   .var = NULL,   .df_row = NULL,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences — count_occurrences","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . id (string) subject variable name. drop (flag) whether non-appearing occurrence levels dropped resulting table. Note case remaining occurrence levels table sorted alphabetically. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count', 'count_fraction', 'count_fraction_fixed_dp', 'fraction' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. denom (string) choice denominator patient proportions. Can : N_col: total number patients column across rows n: number patients occurrences .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .df_row (data.frame) data frame across columns given row split. .var, var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences — count_occurrences","text":"count_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences() table layout. summarize_occurrences() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences() table layout. s_count_occurrences() returns list : count: list counts one element per occurrence. count_fraction: list counts fractions one element per occurrence. fraction: list numerators denominators one element per occurrence. a_count_occurrences() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences — count_occurrences","text":"count_occurrences(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences(): Statistics function counts number patients report occurrence. a_count_occurrences(): Formatted analysis function used afun count_occurrences().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count occurrences — count_occurrences","text":"default, occurrences appear given row split dropped table occurrences table sorted alphabetically per row split. Therefore, corresponding layout needs use split_fun = drop_split_levels split_rows_by calls. Use drop = FALSE like show occurrences.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences — count_occurrences","text":"","code":"library(dplyr) df <- data.frame(   USUBJID = as.character(c(     1, 1, 2, 4, 4, 4,     6, 6, 6, 7, 7, 8   )),   MHDECOD = c(     \"MH1\", \"MH2\", \"MH1\", \"MH1\", \"MH1\", \"MH3\",     \"MH2\", \"MH2\", \"MH3\", \"MH1\", \"MH2\", \"MH4\"   ),   ARM = rep(c(\"A\", \"B\"), each = 6),   SEX = c(\"F\", \"F\", \"M\", \"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\") ) df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Create table layout lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences(vars = \"MHDECOD\", .stats = c(\"count_fraction\"))  # Apply table layout to data and produce `rtable` object tbl <- lyt %>%   build_table(df, alt_counts_df = df_adsl) %>%   prune_table()  tbl #>           A           B     #>         (N=3)       (N=3)   #> ——————————————————————————— #> MH1   3 (100%)    1 (33.3%) #> MH2   1 (33.3%)   2 (66.7%) #> MH3   1 (33.3%)   1 (33.3%) #> MH4       0       1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"SEX\", child_labels = \"visible\") %>%   summarize_occurrences(     var = \"MHDECOD\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>          all obs  #>           (N=6)   #> ————————————————— #> F                 #>   MH1   1 (16.7%) #>   MH2   2 (33.3%) #>   MH3   1 (16.7%) #>   MH4   1 (16.7%) #> M                 #>   MH1   3 (50.0%) #>   MH2   1 (16.7%) #>   MH3   1 (16.7%)  # Count unique occurrences per subject. s_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> $count #> $count$MH1 #> [1] 4 #>  #> $count$MH2 #> [1] 3 #>  #> $count$MH3 #> [1] 2 #>  #> $count$MH4 #> [1] 1 #>  #>  #> $count_fraction #> $count_fraction$MH1 #> [1] 4 1 #>  #> $count_fraction$MH2 #> [1] 3.00 0.75 #>  #> $count_fraction$MH3 #> [1] 2.0 0.5 #>  #> $count_fraction$MH4 #> [1] 1.00 0.25 #>  #>  #> $fraction #> $fraction$MH1 #>   num denom  #>     4     4  #>  #> $fraction$MH2 #>   num denom  #>     3     4  #>  #> $fraction$MH3 #>   num denom  #>     2     4  #>  #> $fraction$MH4 #>   num denom  #>     1     4  #>  #>   a_count_occurrences(   df,   .N_col = 4L,   .df_row = df,   .var = \"MHDECOD\",   id = \"USUBJID\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1       MH1              4          0       MH1 #> 2       MH2              3          0       MH2 #> 3       MH3              2          0       MH3 #> 4       MH4              1          0       MH4 #> 5       MH1       4 (100%)          0       MH1 #> 6       MH2        3 (75%)          0       MH2 #> 7       MH3        2 (50%)          0       MH3 #> 8       MH4        1 (25%)          0       MH4 #> 9       MH1       4 (100%)          0       MH1 #> 10      MH2      3 (75.0%)          0       MH2 #> 11      MH3      2 (50.0%)          0       MH3 #> 12      MH4      1 (25.0%)          0       MH4 #> 13      MH1   4/4 (100.0%)          0       MH1 #> 14      MH2    3/4 (75.0%)          0       MH2 #> 15      MH3    2/4 (50.0%)          0       MH3 #> 16      MH4    1/4 (25.0%)          0       MH4"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Count occurrences by grade — count_occurrences_by_grade","title":"Count occurrences by grade — count_occurrences_by_grade","text":"analyze function count_occurrences_by_grade() creates layout element calculate occurrence counts grade. function analyzes primary analysis variable var indicates toxicity grades. id variable used indicate unique subject identifiers (defaults USUBJID). user can also supply list custom groups grades analyze via grade_groups parameter. remove_single  argument remove single grades analysis grade groups analyzed. multiple grades recorded one patient highest grade level counted. summarize function summarize_occurrences_by_grade() performs function count_occurrences_by_grade() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"count_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   var_labels = var,   show_labels = \"default\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = var,   .stats = NULL,   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  summarize_occurrences_by_grade(   lyt,   var,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   na_str = default_na_str(),   ...,   .stats = NULL,   .formats = NULL,   .indent_mods = NULL,   .labels = NULL )  s_count_occurrences_by_grade(   df,   .var,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   labelstr = \"\" )  a_count_occurrences_by_grade(   df,   .var,   .N_col,   id = \"USUBJID\",   grade_groups = list(),   remove_single = TRUE,   only_grade_groups = FALSE,   labelstr = \"\" )"},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count occurrences by grade — count_occurrences_by_grade","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. grade_groups (named list character) list containing groupings grades. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE). var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'count_fraction', 'count_fraction_fixed_dp' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. .labels (named character) labels statistics (without indent). df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_occurrences_by_grade() table layout. summarize_occurrences_by_grade() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_occurrences_by_grade() table layout. s_count_occurrences_by_grade() returns list counts fractions one element per grade level grade level grouping. a_count_occurrences_by_grade() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count occurrences by grade — count_occurrences_by_grade","text":"count_occurrences_by_grade(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_occurrences_by_grade(): Layout-creating function can take content function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_occurrences_by_grade(): Statistics function counts number patients highest grade. a_count_occurrences_by_grade(): Formatted analysis function used afun count_occurrences_by_grade().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_occurrences_by_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count occurrences by grade — count_occurrences_by_grade","text":"","code":"library(dplyr)  df <- data.frame(   USUBJID = as.character(c(1:6, 1)),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"A\"), levels = c(\"A\", \"B\")),   AETOXGR = factor(c(1, 2, 3, 4, 1, 2, 3), levels = c(1:5)),   AESEV = factor(     x = c(\"MILD\", \"MODERATE\", \"SEVERE\", \"MILD\", \"MILD\", \"MODERATE\", \"SEVERE\"),     levels = c(\"MILD\", \"MODERATE\", \"SEVERE\")   ),   stringsAsFactors = FALSE )  df_adsl <- df %>%   select(USUBJID, ARM) %>%   unique()  # Layout creating function with custom format. basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                  A               B       #>                (N=3)           (N=3)     #> ———————————————————————————————————————— #> MILD       0.00 (0.00%)    2.00 (66.67%) #> MODERATE   1.00 (33.33%)   1.00 (33.33%) #> SEVERE     2.00 (66.67%)   0.00 (0.00%)   # Define additional grade groupings. grade_groups <- list(   \"-Any-\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 1-2\" = c(\"1\", \"2\"),   \"Grade 3-5\" = c(\"3\", \"4\", \"5\") )  basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups,     only_grade_groups = TRUE   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 A           B     #>               (N=3)       (N=3)   #> ————————————————————————————————— #> -Any-       3 (100%)    3 (100%)  #> Grade 1-2   1 (33.3%)   2 (66.7%) #> Grade 3-5   2 (66.7%)   1 (33.3%)  # Layout creating function with custom format. basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AESEV\",     .formats = c(\"count_fraction\" = \"xx.xx (xx.xx%)\")   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                 all obs    #>                  (N=6)     #> —————————————————————————— #> A                          #>   MILD       0.00 (0.00%)  #>   MODERATE   1.00 (16.67%) #>   SEVERE     2.00 (33.33%) #> B                          #>   MILD       2.00 (33.33%) #>   MODERATE   1.00 (16.67%) #>   SEVERE     0.00 (0.00%)   basic_table() %>%   add_colcounts() %>%   split_rows_by(\"ARM\", child_labels = \"visible\", nested = TRUE) %>%   summarize_occurrences_by_grade(     var = \"AETOXGR\",     grade_groups = grade_groups   ) %>%   build_table(df, alt_counts_df = df_adsl) #>                all obs  #>                 (N=6)   #> ——————————————————————— #> A                       #>   -Any-       3 (50.0%) #>   Grade 1-2   1 (16.7%) #>   1               0     #>   2           1 (16.7%) #>   Grade 3-5   2 (33.3%) #>   3           2 (33.3%) #>   4               0     #>   5               0     #> B                       #>   -Any-       3 (50.0%) #>   Grade 1-2   2 (33.3%) #>   1           1 (16.7%) #>   2           1 (16.7%) #>   Grade 3-5   1 (16.7%) #>   3               0     #>   4           1 (16.7%) #>   5               0      s_count_occurrences_by_grade(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> $count_fraction #> $count_fraction$ANY #> [1] 6.0 0.6 #>  #> $count_fraction$`1` #> [1] 1.0 0.1 #>  #> $count_fraction$`2` #> [1] 2.0 0.2 #>  #> $count_fraction$`3` #> [1] 2.0 0.2 #>  #> $count_fraction$`4` #> [1] 1.0 0.1 #>  #> $count_fraction$`5` #> [1] 0 0 #>  #>   #  We need to ungroup `count_fraction` first so that the `rtables` formatting # function `format_count_fraction()` can be applied correctly. afun <- make_afun(a_count_occurrences_by_grade, .ungroup_stats = \"count_fraction\") afun(   df,   .N_col = 10L,   .var = \"AETOXGR\",   id = \"USUBJID\",   grade_groups = list(\"ANY\" = levels(df$AETOXGR)) ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1      ANY      6 (60.0%)          0       ANY #> 2        1      1 (10.0%)          0         1 #> 3        2      2 (20.0%)          0         2 #> 4        3      2 (20.0%)          0         3 #> 5        4      1 (10.0%)          0         4 #> 6        5              0          0         5"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count patient events in columns — count_patients_events_in_cols","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize function summarize_patients_events_in_cols() creates layout element summarize patient event counts columns. function analyzes elements (events) supplied via filters_list parameter returns row counts number patients event well total numbers patients events. id variable used indicate unique subject identifiers (defaults USUBJID). multiple occurrences event recorded patient, event counted .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"summarize_patients_events_in_cols(   lyt,   id = \"USUBJID\",   filters_list = list(),   empty_stats = character(),   na_str = default_na_str(),   ...,   .stats = c(\"unique\", \"all\", names(filters_list)),   .labels = c(unique = \"Patients (All)\", all = \"Events (All)\",     labels_or_names(filters_list)),   col_split = TRUE )  s_count_patients_and_multiple_events(   df,   id,   filters_list,   empty_stats = character(),   labelstr = \"\",   custom_label = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count patient events in columns — count_patients_events_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . id (string) subject variable name. filters_list (named list character) list element list describes one type event describe filters, format s_count_patients_with_event(). label, used column title. empty_stats (character) optional names statistics returned empty corresponding table cells stay blank. na_str (string) string used replace NA empty values output. ... additional arguments lower level functions. .stats (character) statistics select table. addition statistics added using filters_list, statistic options : 'unique', '' .labels (named character) labels statistics (without indent). col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. custom_label (string NULL) provided labelstr empty used label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows containing statistics s_count_patients_and_multiple_events() table layout. s_count_patients_and_multiple_events() returns list statistics: unique: number unique patients df. : number rows df. one element name filters_list: number rows df, .e. events, fulfilling filter condition.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count patient events in columns — count_patients_events_in_cols","text":"summarize_patients_events_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_count_patients_and_multiple_events(): Statistics function counts numbers patients multiple events defined filters. Used analysis function afun summarize_patients_events_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_events_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count patient events in columns — count_patients_events_in_cols","text":"","code":"df <- data.frame(   USUBJID = rep(c(\"id1\", \"id2\", \"id3\", \"id4\"), c(2, 3, 1, 1)),   ARM = c(\"A\", \"A\", \"B\", \"B\", \"B\", \"B\", \"A\"),   AESER = rep(\"Y\", 7),   AESDTH = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"N\"),   AEREL = c(\"Y\", \"Y\", \"N\", \"Y\", \"Y\", \"N\", \"Y\"),   AEDECOD = c(\"A\", \"A\", \"A\", \"B\", \"B\", \"C\", \"D\"),   AEBODSYS = rep(c(\"SOC1\", \"SOC2\", \"SOC3\"), c(3, 3, 1)) )  # `summarize_patients_events_in_cols()` basic_table() %>%   summarize_patients_events_in_cols(     filters_list = list(       related = formatters::with_label(c(AEREL = \"Y\"), \"Events (Related)\"),       fatal = c(AESDTH = \"Y\"),       fatal_related = c(AEREL = \"Y\", AESDTH = \"Y\")     ),     custom_label = \"%s Total number of patients and events\"   ) %>%   build_table(df) #>                                          Patients (All)   Events (All)   Events (Related)   fatal   fatal_related #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> %s Total number of patients and events         4               7                5             4           4"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with a particular event — count_patients_with_event","title":"Count the number of patients with a particular event — count_patients_with_event","text":"analyze function count_patients_with_event() creates layout element calculate patient counts user-specified set events. function analyzes primary analysis variable vars indicates unique subject identifiers. Events defined user named vector via filters argument, name corresponds variable value value(s) variable takes event. multiple records event recorded patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"count_patients_with_event(   lyt,   vars,   filters,   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  a_count_patients_with_event(   df,   .var,   filters,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with a particular event — count_patients_with_event","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . filters (character) character vector specifying column names flag variables used counting number unique identifiers satisfying conditions. Multiple column names flags accepted format c(\"column_name1\" = \"flag1\", \"column_name2\" = \"flag2\"). Note equality accepted condition. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_event() table layout. s_count_patients_with_event() returns count fraction unique identifiers defined event. a_count_patients_with_event() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with a particular event — count_patients_with_event","text":"count_patients_with_event(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_event(): Statistics function counts number patients defined event occurred. a_count_patients_with_event(): Formatted analysis function used afun count_patients_with_event().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_event.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with a particular event — count_patients_with_event","text":"","code":"# `count_patients_with_event()`  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_values(     \"STUDYID\",     values = \"AB12345\",     .stats = \"count\",     .labels = c(count = \"Total AEs\")   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with at least one adverse event\"),     table_names = \"tbl_all\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),     .labels = c(count_fraction = \"Total number of patients with fatal AEs\"),     table_names = \"tbl_fatal\"   ) %>%   count_patients_with_event(     \"SUBJID\",     filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\", \"AEREL\" = \"Y\"),     .labels = c(count_fraction = \"Total number of patients with related fatal AEs\"),     .indent_mods = c(count_fraction = 2L),     table_names = \"tbl_rel_fatal\"   )  build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                     202          177            162       #> Total number of patients with at least one adverse event   59 (100%)    57 (100%)      48 (100%)    #> Total number of patients with fatal AEs                    28 (47.5%)   31 (54.4%)     20 (41.7%)   #>     Total number of patients with related fatal AEs        28 (47.5%)   31 (54.4%)     20 (41.7%)    # `s_count_patients_with_event()`  s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\") ) #> $n #> [1] 164 #>  #> $count #> [1] 164 #>  #> $count_fraction #> [1] 164   1 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\") ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.4817073 #>  #> $n_blq #> [1] 0 #>   s_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\", \"AEOUT\" = \"FATAL\"),   denom = \"N_col\",   .N_col = 456 ) #> $n #> [1] 164 #>  #> $count #> [1] 79 #>  #> $count_fraction #> [1] 79.0000000  0.1732456 #>  #> $n_blq #> [1] 0 #>   # `a_count_patients_with_event()`  a_count_patients_with_event(   tern_ex_adae,   .var = \"SUBJID\",   filters = c(\"TRTEMFL\" = \"Y\"),   .N_col = 100,   .N_row = 100 ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n            164          0              n #> 2          count            164          0          count #> 3 count_fraction     164 (100%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":null,"dir":"Reference","previous_headings":"","what":"Count the number of patients with particular flags — count_patients_with_flags","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"analyze function count_patients_with_flags() creates layout element calculate counts patients user-specified flags present. function analyzes primary analysis variable var indicates unique subject identifiers. Flags variables analyze specified user via flag_variables argument, must either take value TRUE (flag present) FALSE (flag absent) record. multiple records flag present patient, one occurrence counted.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"count_patients_with_flags(   lyt,   var,   flag_variables,   flag_labels = NULL,   var_labels = var,   show_labels = \"hidden\",   riskdiff = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = paste0(\"tbl_flags_\", var),   .stats = \"count_fraction\",   .formats = NULL,   .indent_mods = NULL )  s_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  a_count_patients_with_flags(   df,   .var,   flag_variables,   flag_labels = NULL,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. flag_variables (character) vector specifying names logical variables analysis dataset used counting number unique identifiers. flag_labels (character) vector labels use flag variables. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) name column contains unique identifier. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_patients_with_flags() table layout. s_count_patients_with_flags() returns count fraction unique identifiers particular flag list statistics n, count, count_fraction, n_blq, one element per flag. a_count_patients_with_flags() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"count_patients_with_flags(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_patients_with_flags(): Statistics function counts number patients particular flag variable TRUE. a_count_patients_with_flags(): Formatted analysis function used afun count_patients_with_flags().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"flag_labels specified, variables labels extracted df. variables labeled, variable names used instead. Alternatively, named vector can supplied flag_variables within name-value pair name corresponds variable name value label use variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/count_patients_with_flags.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count the number of patients with particular flags — count_patients_with_flags","text":"","code":"library(dplyr)  # Add labelled flag variables to analysis dataset. adae <- tern_ex_adae %>%   mutate(     fl1 = TRUE %>% with_label(\"Total AEs\"),     fl2 = (TRTEMFL == \"Y\") %>%       with_label(\"Total number of patients with at least one adverse event\"),     fl3 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\") %>%       with_label(\"Total number of patients with fatal AEs\"),     fl4 = (TRTEMFL == \"Y\" & AEOUT == \"FATAL\" & AEREL == \"Y\") %>%       with_label(\"Total number of patients with related fatal AEs\")   )  # `count_patients_with_flags()`  lyt2 <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   count_patients_with_flags(     \"SUBJID\",     flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),     denom = \"N_col\"   )  build_table(lyt2, adae, alt_counts_df = tern_ex_adsl) #>                                                            A: Drug X    B: Placebo   C: Combination #>                                                              (N=69)       (N=73)         (N=58)     #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Total AEs                                                  59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with at least one adverse event   59 (85.5%)   57 (78.1%)     48 (82.8%)   #> Total number of patients with fatal AEs                    28 (40.6%)   31 (42.5%)     20 (34.5%)   #> Total number of patients with related fatal AEs            28 (40.6%)   31 (42.5%)     20 (34.5%)    # `s_count_patients_with_flags()`  s_count_patients_with_flags(   adae,   \"SUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\"),   denom = \"N_col\",   .N_col = 1000 ) #> $n #> $n$`Total AEs` #> [1] 164 #>  #> $n$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $n$`Total number of patients with fatal AEs` #> [1] 164 #>  #> $n$`Total number of patients with related fatal AEs` #> [1] 164 #>  #>  #> $count #> $count$`Total AEs` #> [1] 164 #>  #> $count$`Total number of patients with at least one adverse event` #> [1] 164 #>  #> $count$`Total number of patients with fatal AEs` #> [1] 79 #>  #> $count$`Total number of patients with related fatal AEs` #> [1] 79 #>  #>  #> $count_fraction #> $count_fraction$`Total AEs` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with at least one adverse event` #> [1] 164.000   0.164 #>  #> $count_fraction$`Total number of patients with fatal AEs` #> [1] 79.000  0.079 #>  #> $count_fraction$`Total number of patients with related fatal AEs` #> [1] 79.000  0.079 #>  #>  #> $n_blq #> $n_blq$`Total AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with at least one adverse event` #> [1] 0 #>  #> $n_blq$`Total number of patients with fatal AEs` #> [1] 0 #>  #> $n_blq$`Total number of patients with related fatal AEs` #> [1] 0 #>  #>   #  We need to ungroup `count_fraction` first so that the `rtables` formatting # function `format_count_fraction()` can be applied correctly.  # `a_count_patients_with_flags()`  afun <- make_afun(a_count_patients_with_flags,   .stats = \"count_fraction\",   .ungroup_stats = \"count_fraction\" ) afun(   adae,   .N_col = 10L,   .N_row = 10L,   .var = \"USUBJID\",   flag_variables = c(\"fl1\", \"fl2\", \"fl3\", \"fl4\") ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>                                                   row_name formatted_cell #> 1                                                Total AEs     164 (100%) #> 2 Total number of patients with at least one adverse event     164 (100%) #> 3                  Total number of patients with fatal AEs     79 (48.2%) #> 4          Total number of patients with related fatal AEs     79 (48.2%) #>   indent_mod                                                row_label #> 1          0                                                Total AEs #> 2          0 Total number of patients with at least one adverse event #> 3          0                  Total number of patients with fatal AEs #> 4          0          Total number of patients with related fatal AEs"},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Count specific values — count_values","title":"Count specific values — count_values","text":"analyze function count_values() creates layout element calculate counts specific values within variable interest. function analyzes one variables interest supplied vector vars. Values count variable(s) vars can given vector via values argument. One row counts generated variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count specific values — count_values","text":"","code":"count_values(   lyt,   vars,   values,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = \"count_fraction\",   .formats = NULL,   .labels = c(count_fraction = paste(values, collapse = \", \")),   .indent_mods = NULL )  s_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )  # S3 method for class 'character' s_count_values(x, values = \"Y\", na.rm = TRUE, ...)  # S3 method for class 'factor' s_count_values(x, values = \"Y\", ...)  # S3 method for class 'logical' s_count_values(x, values = TRUE, ...)  a_count_values(   x,   values,   na.rm = TRUE,   .N_col,   .N_row,   denom = c(\"n\", \"N_row\", \"N_col\") )"},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count specific values — count_values","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . values (character) specific values counted. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'count', 'count_fraction', 'count_fraction_fixed_dp', 'n_blq' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .N_row (integer(1)) row-wise N (row group count) group observations analyzed (.e. column-based subsetting) typically passed rtables. denom (string) choice denominator proportion. Options : n: number values row column intersection. N_row: total number values row across columns. N_col: total number values column across rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count specific values — count_values","text":"count_values() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_count_values() table layout. s_count_values() returns output s_summary() specified values non-numeric variable. a_count_values() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count specific values — count_values","text":"count_values(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_count_values(): S3 generic function count values. s_count_values(character): Method character class. s_count_values(factor): Method factor class. makes automatic conversion character forwards method characters. s_count_values(logical): Method logical class. a_count_values(): Formatted analysis function used afun count_values().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count specific values — count_values","text":"factor variables, s_count_values checks whether values included levels x fails otherwise. count_values(), variable labels shown one element vars, otherwise hidden.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/count_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count specific values — count_values","text":"","code":"# `count_values` basic_table() %>%   count_values(\"Species\", values = \"setosa\") %>%   build_table(iris) #>            all obs   #> ———————————————————— #> setosa   50 (33.33%)  # `s_count_values.character` s_count_values(x = c(\"a\", \"b\", \"a\"), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>  s_count_values(x = c(\"a\", \"b\", \"a\", NA, NA), values = \"b\", na.rm = FALSE) #> $n #> [1] 5 #>  #> $count #> [1] 1 #>  #> $count_fraction #> [1] 1.0 0.2 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.factor` s_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\") #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `s_count_values.logical` s_count_values(x = c(TRUE, FALSE, TRUE)) #> $n #> [1] 3 #>  #> $count #> [1] 2 #>  #> $count_fraction #> [1] 2.0000000 0.6666667 #>  #> $n_blq #> [1] 0 #>   # `a_count_values` a_count_values(x = factor(c(\"a\", \"b\", \"a\")), values = \"a\", .N_col = 10, .N_row = 10) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>         row_name formatted_cell indent_mod      row_label #> 1              n              3          0              n #> 2          count              2          0          count #> 3 count_fraction     2 (66.67%)          0 count_fraction #> 4          n_blq              0          0          n_blq"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox proportional hazards regression — cox_regression","title":"Cox proportional hazards regression — cox_regression","text":"Fits Cox regression model estimates hazard ratio describe effect size survival analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox proportional hazards regression — cox_regression","text":"","code":"summarize_coxreg(   lyt,   variables,   control = control_coxreg(),   at = list(),   multivar = FALSE,   common_var = \"STUDYID\",   .stats = c(\"n\", \"hr\", \"ci\", \"pval\", \"pval_inter\"),   .formats = c(n = \"xx\", hr = \"xx.xx\", ci = \"(xx.xx, xx.xx)\", pval =     \"x.xxxx | (<0.0001)\", pval_inter = \"x.xxxx | (<0.0001)\"),   varlabels = NULL,   .indent_mods = NULL,   na_str = \"\",   .section_div = NA_character_ )  s_coxreg(model_df, .stats, .which_vars = \"all\", .var_nms = NULL)  a_coxreg(   df,   labelstr,   eff = FALSE,   var_main = FALSE,   multivar = FALSE,   variables,   at = list(),   control = control_coxreg(),   .spl_context,   .stats,   .formats,   .indent_mods = NULL,   na_str = \"\",   cache_env = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox proportional hazards regression — cox_regression","text":"lyt (PreDataTableLayouts) layout analyses added . variables (named list string) list additional analysis variables. control (list) list parameters returned helper function control_coxreg(). (list numeric) candidate covariate numeric, use specify value covariate effect estimated. multivar (flag) whether multivariate Cox regression run (defaults FALSE), otherwise univariate Cox regression run. common_var (string) name factor variable dataset takes value rows. created pre-processing variable currently exists. .stats (character) names statistics reported among: n: number observations (univariate ) hr: hazard ratio ci: confidence interval pval: p-value treatment effect pval_inter: p-value interaction effect treatment covariate (univariate ) .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. varlabels (list) named list corresponds names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. na_str (string) custom string replace NA values . Defaults \"\". .section_div (string NA) string repeated section divider sections. Defaults NA section divider. vector two strings given, first used treatment covariate sections second different covariates. model_df (data.frame) contains resulting model fit fit_coxreg function tidying applied via broom::tidy(). .which_vars (character) rows statistics returned given model. Defaults \"\". options include \"var_main\" main effects, \"inter\" interaction effects, \"multi_lvl\" multivariate model covariate level rows. .which_vars \"\", specific variables can selected specifying .var_nms. .var_nms (character) term value rows df .stats returned. Typically name variable. using variable labels, var vector desired variable name variable label order see .stats related variable. .which_vars \"var_main\", .var_nms variable name. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. eff (flag) whether treatment effect calculated. Defaults FALSE. var_main (flag) whether main effects calculated. Defaults FALSE. .spl_context (data.frame) gives information ancestor split states passed rtables. cache_env (environment) environment object used cache regression model order avoid repeatedly fitting model every row table. Defaults NULL (caching).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add Cox regression table containing chosen statistics table layout. s_coxreg() returns selected statistic Cox regression model selected variable(s). a_coxreg() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox proportional hazards regression — cox_regression","text":"Cox models commonly used methods estimate magnitude effect survival analysis. assumes proportional hazards: ratio hazards groups (e.g., two arms) constant time. ratio referred \"hazard ratio\" (HR) one commonly reported metrics describe effect size survival analysis (NEST Team, 2020).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox proportional hazards regression — cox_regression","text":"summarize_coxreg(): Layout-creating function creates Cox regression summary table layout. function wrapper several rtables layouting functions. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). s_coxreg(): Statistics function transforms results tabulated fit_coxreg_univar() fit_coxreg_multivar() list. a_coxreg(): Analysis function used afun rtables::analyze() cfun rtables::summarize_row_groups() within summarize_coxreg().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox proportional hazards regression — cox_regression","text":"","code":"library(survival)  # Testing dataset [survival::bladder]. set.seed(1, kind = \"Mersenne-Twister\") dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   tibble::tibble(     TIME = stop,     STATUS = event,     ARM = as.factor(rx),     COVAR1 = as.factor(enum) %>% formatters::with_label(\"A Covariate Label\"),     COVAR2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     ) %>% formatters::with_label(\"Sex (F/M)\")   ) ) dta_bladder$AGE <- sample(20:60, size = nrow(dta_bladder), replace = TRUE) dta_bladder$STUDYID <- factor(\"X\")  u1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  u2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  m1_variables <- list(   time = \"TIME\", event = \"STATUS\", arm = \"ARM\", covariates = c(\"COVAR1\", \"COVAR2\") )  m2_variables <- list(time = \"TIME\", event = \"STATUS\", covariates = c(\"COVAR1\", \"COVAR2\"))  # summarize_coxreg  result_univar <- basic_table() %>%   summarize_coxreg(variables = u1_variables) %>%   build_table(dta_bladder) result_univar #>                        n    Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————— #> Treatment:                                                        #>   2 vs control (1)    340       0.64       (0.43, 0.94)   0.0242  #> Covariate:                                                        #>   A Covariate Label   340       0.61       (0.41, 0.90)   0.0126  #>   Sex (F/M)           340       0.62       (0.42, 0.92)   0.0182   result_univar_covs <- basic_table() %>%   summarize_coxreg(     variables = u2_variables,   ) %>%   build_table(dta_bladder) result_univar_covs #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.45       (0.28, 0.71)   0.0007  #>     3                                     0.31       (0.19, 0.52)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.33       (0.91, 1.94)   0.1414   result_multivar <- basic_table() %>%   summarize_coxreg(     variables = m1_variables,     multivar = TRUE,   ) %>%   build_table(dta_bladder) result_multivar #>                                       Hazard Ratio      95% CI      p-value #> ——————————————————————————————————————————————————————————————————————————— #> Treatment:                                                                  #>   ARM (reference = 1)                                                       #>     2                                     0.61       (0.41, 0.90)   0.0123  #> Covariate:                                                                  #>   A Covariate Label (reference = 1)                                 <0.0001 #>     2                                     0.46       (0.28, 0.73)   0.0011  #>     3                                     0.31       (0.18, 0.51)   <0.0001 #>     4                                     0.18       (0.10, 0.33)   <0.0001 #>   Sex (F/M) (reference = F)                                                 #>     M                                     1.29       (0.88, 1.89)   0.1911   result_multivar_covs <- basic_table() %>%   summarize_coxreg(     variables = m2_variables,     multivar = TRUE,     varlabels = c(\"Covariate 1\", \"Covariate 2\") # custom labels   ) %>%   build_table(dta_bladder) result_multivar_covs #>                                 Hazard Ratio      95% CI      p-value #> ————————————————————————————————————————————————————————————————————— #> Covariate:                                                            #>   Covariate 1 (reference = 1)                                 <0.0001 #>     2                               0.46       (0.29, 0.74)   0.0012  #>     3                               0.31       (0.19, 0.52)   <0.0001 #>     4                               0.19       (0.10, 0.34)   <0.0001 #>   Covariate 2 (reference = F)                                         #>     M                               1.29       (0.88, 1.88)   0.1958   # s_coxreg  # Univariate univar_model <- fit_coxreg_univar(variables = u1_variables, data = dta_bladder) df1 <- broom::tidy(univar_model)  s_coxreg(model_df = df1, .stats = \"hr\") #> $hr #> $hr$`2 vs control (1)` #> [1] 0.6386426 #>  #>  #> $hr #> $hr$`A Covariate Label` #> [1] 0.607037 #>  #>  #> $hr #> $hr$`Sex (F/M)` #> [1] 0.6242738 #>  #>   # Univariate with interactions univar_model_inter <- fit_coxreg_univar(   variables = u1_variables, control = control_coxreg(interaction = TRUE), data = dta_bladder ) df1_inter <- broom::tidy(univar_model_inter)  s_coxreg(model_df = df1_inter, .stats = \"hr\", .which_vars = \"inter\", .var_nms = \"COVAR1\") #> $hr #> $hr$`  1` #> [1] 0.6284569 #>  #> $hr$`  2` #> [1] 0.5806499 #>  #> $hr$`  3` #> [1] 0.5486103 #>  #> $hr$`  4` #> [1] 0.6910725 #>  #>   # Univariate without treatment arm - only \"COVAR2\" covariate effects univar_covs_model <- fit_coxreg_univar(variables = u2_variables, data = dta_bladder) df1_covs <- broom::tidy(univar_covs_model)  s_coxreg(model_df = df1_covs, .stats = \"hr\", .var_nms = c(\"COVAR2\", \"Sex (F/M)\")) #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.3271 #>  #>   # Multivariate. multivar_model <- fit_coxreg_multivar(variables = m1_variables, data = dta_bladder) df2 <- broom::tidy(multivar_model)  s_coxreg(model_df = df2, .stats = \"pval\", .which_vars = \"var_main\", .var_nms = \"COVAR1\") #> $pval #> $pval$`A Covariate Label (reference = 1)` #> [1] 7.209956e-09 #>  #>  s_coxreg(   model_df = df2, .stats = \"pval\", .which_vars = \"multi_lvl\",   .var_nms = c(\"COVAR1\", \"A Covariate Label\") ) #> $pval #> $pval$`2` #> [1] 0.001120332 #>  #> $pval$`3` #> [1] 6.293725e-06 #>  #> $pval$`4` #> [1] 3.013875e-08 #>  #>   # Multivariate without treatment arm - only \"COVAR1\" main effect multivar_covs_model <- fit_coxreg_multivar(variables = m2_variables, data = dta_bladder) df2_covs <- broom::tidy(multivar_covs_model)  s_coxreg(model_df = df2_covs, .stats = \"hr\") #> $hr #> $hr$`2` #> [1] 0.4600728 #>  #> $hr$`3` #> [1] 0.3100455 #>  #> $hr$`4` #> [1] 0.1854177 #>  #>  #> $hr #> $hr$`A Covariate Label (reference = 1)` #> numeric(0) #>  #>  #> $hr #> $hr$`Sex (F/M) (reference = F)` #> numeric(0) #>  #>  #> $hr #> $hr$M #> [1] 1.285406 #>  #>   a_coxreg(   df = dta_bladder,   labelstr = \"Label 1\",   variables = u1_variables,   .spl_context = list(value = \"COVAR1\"),   .stats = \"n\",   .formats = \"xx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1  Label 1            340          0   Label 1  a_coxreg(   df = dta_bladder,   labelstr = \"\",   variables = u1_variables,   .spl_context = list(value = \"COVAR2\"),   .stats = \"pval\",   .formats = \"xx.xxxx\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>    row_name formatted_cell indent_mod row_label #> 1 Sex (F/M)         0.0182          0 Sex (F/M)"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":null,"dir":"Reference","previous_headings":"","what":"Cox regression helper function for interactions — cox_regression_inter","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Test estimate effect treatment interaction covariate. effect estimated HR tested treatment given level covariate, comparison treatment control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"h_coxreg_inter_effect(x, effect, covar, mod, label, control, ...)  # S3 method for class 'numeric' h_coxreg_inter_effect(x, effect, covar, mod, label, control, at, ...)  # S3 method for class 'factor' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  # S3 method for class 'character' h_coxreg_inter_effect(x, effect, covar, mod, label, control, data, ...)  h_coxreg_extract_interaction(effect, covar, mod, data, at, control)  h_coxreg_inter_estimations(   variable,   given,   lvl_var,   lvl_given,   mod,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cox regression helper function for interactions — cox_regression_inter","text":"x (numeric factor) values covariate tested. effect (string) name effect tested estimated. covar (string) name covariate model. mod (coxph) fitted Cox regression model (see survival::coxph()). label (string) label returned term_label. control (list) list controls returned control_coxreg(). ... see methods. (list) list items named covariate, every item vector levels interaction estimated. data (data.frame) data frame model fit. variable, given (string) name variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect() returns data.frame covariate interaction effects consisting following variables: effect, term, term_label, level, n, hr, lcl, ucl, pval, pval_inter. h_coxreg_extract_interaction() returns result interaction test estimated values. interaction, h_coxreg_univar_extract() applied instead. h_coxreg_inter_estimations() returns list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female) model abbreviated: y ~ Arm + Sex + Arm:Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) estimation Hazard Ratio arm C/sex M given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5). interaction coefficient deduced b2 + b5 standard error obtained $sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Cox regression helper function for interactions — cox_regression_inter","text":"h_coxreg_inter_effect(): S3 generic helper function determine interaction effect. h_coxreg_inter_effect(numeric): Method numeric class. Estimates interaction numeric covariate. h_coxreg_inter_effect(factor): Method factor class. Estimate interaction factor covariate. h_coxreg_inter_effect(character): Method character class. Estimate interaction character covariate. makes automatic conversion factor forwards method factors. h_coxreg_extract_interaction(): higher level function get results interaction test estimated values. h_coxreg_inter_estimations(): Hazard ratio estimation interactions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cox regression helper function for interactions — cox_regression_inter","text":"Automatic conversion character factor guarantee results can generated correctly. therefore better always pre-process dataset factors manually created character variables passing dataset rtables::build_table().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cox_regression_inter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cox regression helper function for interactions — cox_regression_inter","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4,       labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) h_coxreg_extract_interaction(   mod = mod, effect = \"armcd\", covar = \"covar1\", data = dta_bladder,   control = control_coxreg() ) #>                    effect   term        term_label level   n        hr #> 1              Covariate: covar1 A Covariate Label       340        NA #> armcd2/covar11 Covariate: covar1                 1     1  NA 0.6341111 #> armcd2/covar12 Covariate: covar1                 2     2  NA 0.5845305 #> armcd2/covar13 Covariate: covar1                 3     3  NA 0.5507703 #> armcd2/covar14 Covariate: covar1                 4     4  NA 0.6910643 #>                      lcl      ucl      pval pval_inter #> 1                     NA       NA 0.1302825   0.988245 #> armcd2/covar11 0.3514676 1.144051        NA         NA #> armcd2/covar12 0.2716689 1.257692        NA         NA #> armcd2/covar13 0.2244668 1.351415        NA         NA #> armcd2/covar14 0.2315248 2.062715        NA         NA  mod <- coxph(Surv(time, status) ~ armcd * covar1, data = dta_bladder) result <- h_coxreg_inter_estimations(   variable = \"armcd\", given = \"covar1\",   lvl_var = levels(dta_bladder$armcd),   lvl_given = levels(dta_bladder$covar1),   mod = mod, conf_level = .95 ) result #> $armcd2 #>                      coef  se(coef)        hr       lcl      ucl #> armcd2/covar11 -0.4555312 0.3010803 0.6341111 0.3514676 1.144051 #> armcd2/covar12 -0.5369464 0.3909383 0.5845305 0.2716689 1.257692 #> armcd2/covar13 -0.5964375 0.4579624 0.5507703 0.2244668 1.351415 #> armcd2/covar14 -0.3695225 0.5579418 0.6910643 0.2315248 2.062715 #>  #> attr(,\"details\") #> [1] \"Estimations of armcd hazard ratio given the level of covar1 compared to armcd level 1.\""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":null,"dir":"Reference","previous_headings":"","what":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"cuts numeric vector sample quantile bins.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"cut_quantile_bins(   x,   probs = c(0.25, 0.5, 0.75),   labels = NULL,   type = 7,   ordered = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"x (numeric) continuous variable values cut quantile bins. may contain NA values, used quantile calculations, included return vector. probs (numeric) probabilities identifying quantiles. sorted vector unique proportion values, .e. 0 1, boundaries 0 1 must included. labels (character) unique labels quantile bins. n probabilities probs, must n + 1 long. type (integer(1)) type quantiles use, see stats::quantile() details. ordered (flag) result ordered factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"factor variable appropriately-labeled bins levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"Intervals closed right side. , first bin interval [-Inf, q1] q1 first quantile, second bin (q1, q2], etc., last bin (qn, +Inf] qn last quantile.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/cut_quantile_bins.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cut numeric vector into empirical quantile bins — cut_quantile_bins","text":"","code":"# Default is to cut into quartile bins. cut_quantile_bins(cars$speed) #>  [1] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #>  [7] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   #> [13] [0%,25%]   [0%,25%]   [0%,25%]   (25%,50%]  (25%,50%]  (25%,50%]  #> [19] (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [25] (25%,50%]  (25%,50%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [31] (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  (50%,75%]  #> [37] (50%,75%]  (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [43] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [49] (75%,100%] (75%,100%] #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%]  # Use custom quantiles. cut_quantile_bins(cars$speed, probs = c(0.1, 0.2, 0.6, 0.88)) #>  [1] [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   [0%,10%]   (10%,20%]  #>  [7] (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (10%,20%]  (20%,60%]  #> [13] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [19] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [25] (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  (20%,60%]  #> [31] (20%,60%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [37] (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  (60%,88%]  #> [43] (60%,88%]  (60%,88%]  (88%,100%] (88%,100%] (88%,100%] (88%,100%] #> [49] (88%,100%] (88%,100%] #> Levels: [0%,10%] < (10%,20%] < (20%,60%] < (60%,88%] < (88%,100%]  # Use custom labels. cut_quantile_bins(cars$speed, labels = paste0(\"Q\", 1:4)) #>  [1] Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q1 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 Q2 #> [26] Q2 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q3 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 Q4 #> Levels: Q1 < Q2 < Q3 < Q4  # NAs are preserved in result factor. ozone_binned <- cut_quantile_bins(airquality$Ozone) which(is.na(ozone_binned)) #>  [1]   5  10  25  26  27  32  33  34  35  36  37  39  42  43  45  46  52  53  54 #> [20]  55  56  57  58  59  60  61  65  72  75  83  84 102 103 107 115 119 150 # So you might want to make these explicit. explicit_na(ozone_binned) #>   [1] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   <Missing>  (25%,50%]  #>   [7] (25%,50%]  (25%,50%]  [0%,25%]   <Missing>  [0%,25%]   [0%,25%]   #>  [13] [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  [0%,25%]   #>  [19] (25%,50%]  [0%,25%]   [0%,25%]   [0%,25%]   [0%,25%]   (50%,75%]  #>  [25] <Missing>  <Missing>  <Missing>  (25%,50%]  (50%,75%]  (75%,100%] #>  [31] (50%,75%]  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [37] <Missing>  (25%,50%]  <Missing>  (75%,100%] (50%,75%]  <Missing>  #>  [43] <Missing>  (25%,50%]  <Missing>  <Missing>  (25%,50%]  (50%,75%]  #>  [49] (25%,50%]  [0%,25%]   [0%,25%]   <Missing>  <Missing>  <Missing>  #>  [55] <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  <Missing>  #>  [61] <Missing>  (75%,100%] (50%,75%]  (50%,75%]  <Missing>  (75%,100%] #>  [67] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #>  [73] [0%,25%]   (25%,50%]  <Missing>  [0%,25%]   (50%,75%]  (50%,75%]  #>  [79] (50%,75%]  (75%,100%] (50%,75%]  [0%,25%]   <Missing>  <Missing>  #>  [85] (75%,100%] (75%,100%] (25%,50%]  (50%,75%]  (75%,100%] (50%,75%]  #>  [91] (75%,100%] (50%,75%]  (50%,75%]  [0%,25%]   [0%,25%]   (75%,100%] #>  [97] (50%,75%]  (75%,100%] (75%,100%] (75%,100%] (75%,100%] <Missing>  #> [103] <Missing>  (50%,75%]  (25%,50%]  (75%,100%] <Missing>  (25%,50%]  #> [109] (50%,75%]  (25%,50%]  (25%,50%]  (50%,75%]  (25%,50%]  [0%,25%]   #> [115] <Missing>  (50%,75%]  (75%,100%] (75%,100%] <Missing>  (75%,100%] #> [121] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] (75%,100%] #> [127] (75%,100%] (50%,75%]  (50%,75%]  (25%,50%]  (25%,50%]  (25%,50%]  #> [133] (25%,50%]  (50%,75%]  (25%,50%]  (25%,50%]  [0%,25%]   [0%,25%]   #> [139] (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  [0%,25%]   [0%,25%]   #> [145] (25%,50%]  (50%,75%]  [0%,25%]   [0%,25%]   (25%,50%]  <Missing>  #> [151] [0%,25%]   [0%,25%]   (25%,50%]  #> Levels: [0%,25%] < (25%,50%] < (50%,75%] < (75%,100%] < <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":null,"dir":"Reference","previous_headings":"","what":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Description function produces labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(abnormal)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"abnormal (character) values identifying abnormal range level(s) .var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"Abnormal category labels s_count_abnormal_by_baseline().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_abnormal_by_baseline.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description function for s_count_abnormal_by_baseline() — d_count_abnormal_by_baseline","text":"","code":"d_count_abnormal_by_baseline(\"LOW\") #> $not_abnormal #> [1] \"Not low\" #>  #> $abnormal #> [1] \"Low\" #>  #> $total #> [1] \"Total\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of cumulative count — d_count_cumulative","title":"Description of cumulative count — d_count_cumulative","text":"helper function describes analysis s_count_cumulative().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of cumulative count — d_count_cumulative","text":"","code":"d_count_cumulative(threshold, lower_tail = TRUE, include_eq = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of cumulative count — d_count_cumulative","text":"threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of cumulative count — d_count_cumulative","text":"Labels s_count_cumulative().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"","code":"d_count_missed_doses(thresholds)"},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"thresholds (numeric) minimum number missed doses patients .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_count_missed_doses.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description function that calculates labels for s_count_missed_doses() — d_count_missed_doses","text":"d_count_missed_doses() returns named character vector labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of standard oncology response — d_onco_rsp_label","title":"Description of standard oncology response — d_onco_rsp_label","text":"Describe oncology response standard way.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(x)"},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of standard oncology response — d_onco_rsp_label","text":"x (character) standard oncology codes described.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of standard oncology response — d_onco_rsp_label","text":"Response labels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_onco_rsp_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Description of standard oncology response — d_onco_rsp_label","text":"","code":"d_onco_rsp_label(   c(\"CR\", \"PR\", \"SD\", \"NON CR/PD\", \"PD\", \"NE\", \"Missing\", \"<Missing>\", \"NE/Missing\") ) #>                           CR                           PR  #>       Complete Response (CR)        Partial Response (PR)  #>                           SD                    NON CR/PD  #>          Stable Disease (SD) Non-CR or Non-PD (NON CR/PD)  #>                           PD                           NE  #>     Progressive Disease (PD)           Not Evaluable (NE)  #>                      Missing                    <Missing>  #>                      Missing                    <Missing>  #>                   NE/Missing  #>       Missing or unevaluable  #> 9 Levels: Complete Response (CR) Partial Response (PR) ... <Missing>  # Adding some values not considered in d_onco_rsp_label  d_onco_rsp_label(   c(\"CR\", \"PR\", \"hello\", \"hi\") ) #>                     CR                     PR                  hello  #> Complete Response (CR)  Partial Response (PR)                  hello  #>                     hi  #>                     hi  #> Levels: Complete Response (CR) Partial Response (PR) hello hi"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate PK reference dataset — d_pkparam","text":"","code":"d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate PK reference dataset — d_pkparam","text":"data.frame PK parameters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_pkparam.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate PK reference dataset — d_pkparam","text":"","code":"pk_reference_dataset <- d_pkparam()"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the proportion summary — d_proportion","title":"Description of the proportion summary — d_proportion","text":"helper function describes analysis s_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the proportion summary — d_proportion","text":"","code":"d_proportion(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the proportion summary — d_proportion","text":"conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. long (flag) whether long short (default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the proportion summary — d_proportion","text":"String describing analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of method used for proportion comparison — d_proportion_diff","title":"Description of method used for proportion comparison — d_proportion_diff","text":"auxiliary function describes analysis s_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of method used for proportion comparison — d_proportion_diff","text":"","code":"d_proportion_diff(conf_level, method, long = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of method used for proportion comparison — d_proportion_diff","text":"conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. long (flag) whether long (TRUE) short (FALSE, default) description required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of method used for proportion comparison — d_proportion_diff","text":"string describing analysis.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"Internal function check variables included tabulate_rsp_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"","code":"d_rsp_subgroups_colvars(vars, conf_level = NULL, method = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_rsp_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in binary response by subgroup table — d_rsp_subgroups_colvars","text":"list variables tabulate labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"Internal function check variables included tabulate_survival_subgroups() create column labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"","code":"d_survival_subgroups_colvars(vars, conf_level, method, time_unit = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. conf_level (proportion) confidence level interval. method (string) p-value method testing hazard ratio = 1. time_unit (string) label unit median survival time. Default NULL skips displaying unit.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"list variables labels tabulate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_survival_subgroups_colvars.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Labels for column variables in survival duration by subgroup table — d_survival_subgroups_colvars","text":"least one n_tot n_tot_events must provided vars.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Description of the difference test between two proportions — d_test_proportion_diff","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"auxiliary function describes analysis s_test_proportion_diff.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"","code":"d_test_proportion_diff(method)"},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/d_test_proportion_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Description of the difference test between two proportions — d_test_proportion_diff","text":"string describing test p-value derived.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of days to months — day2month","title":"Conversion of days to months — day2month","text":"Conversion days months","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of days to months — day2month","text":"","code":"day2month(x)"},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of days to months — day2month","text":"x (numeric(1)) time days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of days to months — day2month","text":"numeric vector time months.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/day2month.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of days to months — day2month","text":"","code":"x <- c(403, 248, 30, 86) day2month(x) #> [1] 13.2402464  8.1478439  0.9856263  2.8254620"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"function useful label grid grobs (also ggplot2, lattice plots) title, footnote, page numbers.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"decorate_grob(   grob,   titles,   footnotes,   page = \"\",   width_titles = grid::unit(1, \"npc\"),   width_footnotes = grid::unit(1, \"npc\"),   border = TRUE,   padding = grid::unit(rep(1, 4), \"lines\"),   margins = grid::unit(c(1, 0, 1, 0), \"lines\"),   outer_margins = grid::unit(c(2, 1.5, 3, 1.5), \"cm\"),   gp_titles = grid::gpar(),   gp_footnotes = grid::gpar(fontsize = 8),   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grob (grob) grid grob object, optionally NULL grob decoration shown. titles (character) titles given vector strings separated newline wrapped according page width. footnotes (character) footnotes. Uses formatting rules titles. page (string NULL) page numeration. NULL page number displayed. width_titles (grid::unit) width titles. Usually defined available space grid::unit(1, \"npc\"), affected parameter outer_margins. Right margins (outer_margins[4]) need subtracted allowed width. width_footnotes (grid::unit) width footnotes. default margin correction width_titles. border (flag) whether border drawn around plot . padding (grid::unit) padding. unit object length 4. Innermost margin plot (grob) , possibly, border plot. Usually expressed 4 identical values (usually \"lines\"). defaults grid::unit(rep(1, 4), \"lines\"). margins (grid::unit) margins. unit object length 4. Margins plot elements list (e.g. titles, plot, footers). usually expressed 4 \"lines\", lateral ones 0s, top bottom 1s. defaults grid::unit(c(1, 0, 1, 0), \"lines\"). outer_margins (grid::unit) outer margins. unit object length 4. defines general margin plot, considering also decorations like titles, footnotes, page numbers. defaults grid::unit(c(2, 1.5, 3, 1.5), \"cm\"). gp_titles (gpar) gpar object. Mainly used set different \"fontsize\". gp_footnotes (gpar) gpar object. Mainly used set different \"fontsize\". name character identifier grob.  Used find     grob display list /child another grob. gp \"gpar\" object, typically output     call function gpar.  basically     list graphical parameter settings. vp viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"grid grob (gTree).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"titles footnotes ragged, .e. title wrapped individually.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add titles, footnotes, page Number, and a bounding box to a grid grob — decorate_grob","text":"","code":"library(grid)  titles <- c(   \"Edgar Anderson's Iris Data\",   paste(     \"This famous (Fisher's or Anderson's) iris data set gives the measurements\",     \"in centimeters of the variables sepal length and width and petal length\",     \"and width, respectively, for 50 flowers from each of 3 species of iris.\"   ) )  footnotes <- c(   \"The species are Iris setosa, versicolor, and virginica.\",   paste(     \"iris is a data frame with 150 cases (rows) and 5 variables (columns) named\",     \"Sepal.Length, Sepal.Width, Petal.Length, Petal.Width, and Species.\"   ) )  ## empty plot grid.newpage()  grid.draw(   decorate_grob(     NULL,     titles = titles,     footnotes = footnotes,     page = \"Page 4 of 10\"   ) )   # grid p <- gTree(   children = gList(     rectGrob(),     xaxisGrob(),     yaxisGrob(),     textGrob(\"Sepal.Length\", y = unit(-4, \"lines\")),     textGrob(\"Petal.Length\", x = unit(-3.5, \"lines\"), rot = 90),     pointsGrob(iris$Sepal.Length, iris$Petal.Length, gp = gpar(col = iris$Species), pch = 16)   ),   vp = vpStack(plotViewport(), dataViewport(xData = iris$Sepal.Length, yData = iris$Petal.Length)) ) grid.newpage() grid.draw(p)   grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with ggplot2 library(ggplot2)  p_gg <- ggplot2::ggplot(iris, aes(Sepal.Length, Sepal.Width, col = Species)) +   ggplot2::geom_point() p_gg  p <- ggplotGrob(p_gg) grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   ## with lattice library(lattice)  xyplot(Sepal.Length ~ Petal.Length, data = iris, col = iris$Species)  p <- grid.grab()  grid.newpage() grid.draw(   decorate_grob(     grob = p,     titles = titles,     footnotes = footnotes,     page = \"Page 6 of 129\"   ) )   # with gridExtra - no borders library(gridExtra) #>  #> Attaching package: ‘gridExtra’ #> The following object is masked from ‘package:dplyr’: #>  #>     combine grid.newpage() grid.draw(   decorate_grob(     tableGrob(       head(mtcars)     ),     titles = \"title\",     footnotes = \"footnote\",     border = FALSE   ) )"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":null,"dir":"Reference","previous_headings":"","what":"Update page number — decorate_grob_factory","title":"Update page number — decorate_grob_factory","text":"Automatically updates page number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update page number — decorate_grob_factory","text":"","code":"decorate_grob_factory(npages, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update page number — decorate_grob_factory","text":"npages (numeric(1)) total number pages. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_factory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update page number — decorate_grob_factory","text":"Closure increments page number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":null,"dir":"Reference","previous_headings":"","what":"Decorate set of grobs and add page numbering — decorate_grob_set","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"Note uses decorate_grob_factory() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"decorate_grob_set(grobs, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"grobs (list grob) list grid grobs. ... arguments passed decorate_grob().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"decorated grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/decorate_grob_set.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decorate set of grobs and add page numbering — decorate_grob_set","text":"","code":"library(ggplot2) library(grid) g <- with(data = iris, {   list(     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Sepal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Length, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Sepal.Width, Petal.Width, col = Species)) +         ggplot2::geom_point()     ),     ggplot2::ggplotGrob(       ggplot2::ggplot(mapping = aes(Petal.Length, Petal.Width, col = Species)) +         ggplot2::geom_point()     )   ) }) lg <- decorate_grob_set(grobs = g, titles = \"Hello\\nOne\\nTwo\\nThree\", footnotes = \"\")  draw_grob(lg[[1]]) #> Warning: `draw_grob()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects.  draw_grob(lg[[2]])  draw_grob(lg[[6]])"},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":null,"dir":"Reference","previous_headings":"","what":"Default string replacement for NA values — default_na_str","title":"Default string replacement for NA values — default_na_str","text":"default string used represent NA values. value used default value na_str argument throughout tern package, printed place NA values output tables. specified tern function user via na_str argument, R environment options via set_default_na_str(), NA used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Default string replacement for NA values — default_na_str","text":"","code":"default_na_str()  set_default_na_str(na_str)"},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Default string replacement for NA values — default_na_str","text":"na_str (string) single string value set R environment options default value replace NAs. Use getOption(\"tern_default_na_str\") check current value set R environment (defaults NULL set).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Default string replacement for NA values — default_na_str","text":"default_na_str returns current value R environment option set \"tern_default_na_str\", NA_character_ otherwise. set_default_na_str return value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Default string replacement for NA values — default_na_str","text":"default_na_str(): Accessor default NA value replacement string. set_default_na_str(): Setter default NA value replacement string. Sets option \"tern_default_na_str\" within R environment.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_na_str.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Default string replacement for NA values — default_na_str","text":"","code":"# Default settings default_na_str() #> [1] NA getOption(\"tern_default_na_str\") #> NULL  # Set custom value set_default_na_str(\"<Missing>\")  # Settings after value has been set default_na_str() #> [1] \"<Missing>\" getOption(\"tern_default_na_str\") #> [1] \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Utility functions get valid statistic methods different method groups (.stats) associated formats (.formats), labels (.labels), indent modifiers (.indent_mods). utility used across tern, working principles can seen analyze_vars(). See notes understand experimental.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"get_stats(   method_groups = \"analyze_vars_numeric\",   stats_in = NULL,   add_pval = FALSE )  get_formats_from_stats(stats, formats_in = NULL)  get_labels_from_stats(stats, labels_in = NULL, row_nms = NULL)  get_indents_from_stats(stats, indents_in = NULL, row_nms = NULL)  tern_default_stats  tern_default_formats  tern_default_labels  summary_formats(type = \"numeric\", include_pval = FALSE)  summary_labels(type = \"numeric\", include_pval = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"tern_default_stats named list available statistics, element named corresponding statistical method group. tern_default_formats named vector available default formats, element named corresponding statistic. tern_default_labels named character vector available default labels, element named corresponding statistic.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"method_groups (character) indicates statistical method group (tern analyze function) retrieve default statistics . character vector can used specify one statistical method group. stats_in (character) statistics retrieve selected method group. add_pval (flag) \"pval\" (\"pval_counts\" method_groups contains \"analyze_vars_counts\") added statistical methods? stats (character) statistical methods get defaults . formats_in (named vector) inserted formats replace defaults. can character vector formatters::list_valid_format_labels() custom format function. labels_in (named character) inserted labels replace defaults. row_nms (character) row names. Levels factor character variable, statistics .stats calculated . parameter set, variable levels used defaults, names given custom values correspond levels (format statistic.level) instead statistics. Can also variable names rows correspond different variables instead levels. Defaults NULL. indents_in (named vector) inserted indent modifiers replace defaults (default 0L). type (string)\"numeric\" \"counts\". include_pval (flag) add_pval argument get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats() returns character vector statistical methods. get_formats_from_stats() returns named vector formats (present either tern_default_formats formats_in, otherwise NULL). Values can taken formatters::list_valid_format_labels() custom function (e.g. formatting_functions). get_labels_from_stats() returns named character vector labels (present either tern_default_labels labels_in, otherwise NULL). get_indents_from_stats() returns single indent modifier value apply rows named numeric vector indent modifiers (present, otherwise NULL). summary_formats() returns named vector default statistic formats given data type. summary_labels returns named vector default statistic labels given data type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"Current choices type counts numeric analyze_vars() affect get_stats().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"get_stats(): Get statistics available given method group (analyze function). check available defaults see tern::tern_default_stats list. get_formats_from_stats(): Get formats corresponding list statistics. check available defaults see tern::tern_default_formats list. get_labels_from_stats(): Get labels corresponding list statistics. check available defaults see tern::tern_default_labels list. available , statistics name used label. get_indents_from_stats(): Format indent modifiers given vector/list statistics. defaults 0L values. tern_default_stats: Named list available statistics method group tern. tern_default_formats: Named vector default formats tern. tern_default_labels: Named character vector default labels tern. summary_formats():  Quick function retrieve default formats summary statistics: analyze_vars() analyze_vars_in_cols() principally. summary_labels():  Quick function retrieve default labels summary statistics. Returns labels descriptive statistics understood rtables. Similar summary_formats.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"defaults experimental use names functions retrieve default statistics. generalized groups methods according reasonable groupings. Formats tern rtables can functions take table cell value return string. well documented vignette(\"custom_appearance\", package = \"rtables\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/default_stats_formats_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get default statistical methods and their associated formats, labels, and indent modifiers — default_stats_formats_labels","text":"","code":"# analyze_vars is numeric num_stats <- get_stats(\"analyze_vars_numeric\") # also the default  # Other type cnt_stats <- get_stats(\"analyze_vars_counts\")  # Weirdly taking the pval from count_occurrences only_pval <- get_stats(\"count_occurrences\", add_pval = TRUE, stats_in = \"pval\")  # All count_occurrences all_cnt_occ <- get_stats(\"count_occurrences\")  # Multiple get_stats(c(\"count_occurrences\", \"analyze_vars_counts\")) #> [1] \"count\"                   \"count_fraction\"          #> [3] \"count_fraction_fixed_dp\" \"fraction\"                #> [5] \"n\"                       \"n_blq\"                    # Defaults formats get_formats_from_stats(num_stats) #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  get_formats_from_stats(cnt_stats) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  get_formats_from_stats(only_pval) #> $pval #> [1] \"x.xxxx | (<0.0001)\" #>  get_formats_from_stats(all_cnt_occ) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>   # Addition of customs get_formats_from_stats(all_cnt_occ, formats_in = c(\"fraction\" = c(\"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx\" #>  get_formats_from_stats(all_cnt_occ, formats_in = list(\"fraction\" = c(\"xx.xx\", \"xx\"))) #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> [1] \"xx.xx\" \"xx\"    #>   # Defaults labels get_labels_from_stats(num_stats) #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  get_labels_from_stats(cnt_stats) #>                       n                   count          count_fraction  #>                     \"n\"                 \"count\"        \"count_fraction\"  #> count_fraction_fixed_dp                fraction                   n_blq  #>        \"count_fraction\"              \"fraction\"                 \"n_blq\"  get_labels_from_stats(only_pval) #>               pval  #> \"p-value (t-test)\"  get_labels_from_stats(all_cnt_occ) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"fraction\"   # Addition of customs get_labels_from_stats(all_cnt_occ, labels_in = c(\"fraction\" = \"Fraction\")) #>                   count          count_fraction count_fraction_fixed_dp  #>                 \"count\"        \"count_fraction\"        \"count_fraction\"  #>                fraction  #>              \"Fraction\"  get_labels_from_stats(all_cnt_occ, labels_in = list(\"fraction\" = c(\"Some more fractions\"))) #> $count #> [1] \"count\" #>  #> $count_fraction #> [1] \"count_fraction\" #>  #> $count_fraction_fixed_dp #> [1] \"count_fraction\" #>  #> $fraction #> [1] \"Some more fractions\" #>   get_indents_from_stats(all_cnt_occ, indents_in = 3L) #> [1] 3 3 3 3 get_indents_from_stats(all_cnt_occ, indents_in = list(count = 2L, count_fraction = 5L)) #> $count #> [1] 2 #>  #> $count_fraction #> [1] 5 #>  #> $count_fraction_fixed_dp #> [1] 0 #>  #> $fraction #> [1] 0 #>  get_indents_from_stats(   all_cnt_occ,   indents_in = list(a = 2L, count.a = 1L, count.b = 5L), row_nms = c(\"a\", \"b\") ) #> $count.a #> [1] 1 #>  #> $count.b #> [1] 5 #>  #> $count_fraction.a #> [1] 2 #>  #> $count_fraction.b #> [1] 0 #>  #> $count_fraction_fixed_dp.a #> [1] 2 #>  #> $count_fraction_fixed_dp.b #> [1] 0 #>  #> $fraction.a #> [1] 2 #>  #> $fraction.b #> [1] 0 #>   summary_formats() #> Warning: `summary_formats()` was deprecated in tern 0.9.6. #> ℹ Use get_formats_from_stats(get_stats(\"analyze_vars_numeric\", add_pval = #>   include_pval)) instead #> $n #> [1] \"xx.\" #>  #> $sum #> [1] \"xx.x\" #>  #> $mean #> [1] \"xx.x\" #>  #> $sd #> [1] \"xx.x\" #>  #> $se #> [1] \"xx.x\" #>  #> $mean_sd #> [1] \"xx.x (xx.x)\" #>  #> $mean_se #> [1] \"xx.x (xx.x)\" #>  #> $mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sei #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_sdi #> [1] \"(xx.xx, xx.xx)\" #>  #> $mean_pval #> [1] \"x.xxxx | (<0.0001)\" #>  #> $median #> [1] \"xx.x\" #>  #> $mad #> [1] \"xx.x\" #>  #> $median_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $quantiles #> [1] \"xx.x - xx.x\" #>  #> $iqr #> [1] \"xx.x\" #>  #> $range #> [1] \"xx.x - xx.x\" #>  #> $min #> [1] \"xx.x\" #>  #> $max #> [1] \"xx.x\" #>  #> $median_range #> [1] \"xx.x (xx.x - xx.x)\" #>  #> $cv #> [1] \"xx.x\" #>  #> $geom_mean #> [1] \"xx.x\" #>  #> $geom_mean_ci #> [1] \"(xx.xx, xx.xx)\" #>  #> $geom_cv #> [1] \"xx.x\" #>  summary_formats(type = \"counts\", include_pval = TRUE) #> $n #> [1] \"xx.\" #>  #> $count #> [1] \"xx.\" #>  #> $count_fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else { #>     paste0(x[1], \" (\", round(x[2] * 100, 1), \"%)\") #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $count_fraction_fixed_dp #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>  #>   if (any(is.na(x))) { #>     return(\"NA\") #>   } #>  #>   checkmate::assert_vector(x) #>   checkmate::assert_integerish(x[1]) #>   assert_proportion_value(x[2], include_boundaries = TRUE) #>  #>   result <- if (x[1] == 0) { #>     \"0\" #>   } else if (.is_equal_float(x[2], 1)) { #>     sprintf(\"%d (100%%)\", x[1]) #>   } else { #>     sprintf(\"%d (%.1f%%)\", x[1], x[2] * 100) #>   } #>  #>   return(result) #> } #> <environment: namespace:tern> #>  #> $fraction #> function(x, ...) { #>   attr(x, \"label\") <- NULL #>   checkmate::assert_vector(x) #>   checkmate::assert_count(x[\"num\"]) #>   checkmate::assert_count(x[\"denom\"]) #>  #>   result <- if (x[\"num\"] == 0) { #>     paste0(x[\"num\"], \"/\", x[\"denom\"]) #>   } else { #>     paste0( #>       x[\"num\"], \"/\", x[\"denom\"], #>       \" (\", sprintf(\"%.1f\", round(x[\"num\"] / x[\"denom\"] * 100, 1)), \"%)\" #>     ) #>   } #>   return(result) #> } #> <environment: namespace:tern> #>  #> $n_blq #> [1] \"xx.\" #>  #> $pval_counts #> [1] \"x.xxxx | (<0.0001)\" #>   summary_labels() #> Warning: `summary_formats()` was deprecated in tern 0.9.6. #> ℹ Use get_labels_from_stats(get_stats(\"analyze_vars_numeric\", add_pval = #>   include_pval)) instead #>                             n                           sum  #>                           \"n\"                         \"Sum\"  #>                          mean                            sd  #>                        \"Mean\"                          \"SD\"  #>                            se                       mean_sd  #>                          \"SE\"                   \"Mean (SD)\"  #>                       mean_se                       mean_ci  #>                   \"Mean (SE)\"                 \"Mean 95% CI\"  #>                      mean_sei                      mean_sdi  #>               \"Mean -/+ 1xSE\"               \"Mean -/+ 1xSD\"  #>                     mean_pval                        median  #> \"Mean p-value (H0: mean = 0)\"                      \"Median\"  #>                           mad                     median_ci  #>   \"Median Absolute Deviation\"               \"Median 95% CI\"  #>                     quantiles                           iqr  #>             \"25% and 75%-ile\"                         \"IQR\"  #>                         range                           min  #>                   \"Min - Max\"                     \"Minimum\"  #>                           max                  median_range  #>                     \"Maximum\"          \"Median (Min - Max)\"  #>                            cv                     geom_mean  #>                      \"CV (%)\"              \"Geometric Mean\"  #>                  geom_mean_ci                       geom_cv  #>       \"Geometric Mean 95% CI\"         \"CV % Geometric Mean\"  summary_labels(type = \"counts\", include_pval = TRUE) #>                            n                        count  #>                          \"n\"                      \"count\"  #>               count_fraction      count_fraction_fixed_dp  #>             \"count_fraction\"             \"count_fraction\"  #>                     fraction                        n_blq  #>                   \"fraction\"                      \"n_blq\"  #>                  pval_counts  #> \"p-value (chi-squared test)\""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for a difference of binomials — desctools_binom","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"Several confidence intervals difference proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"","code":"desctools_binom(   x1,   n1,   x2,   n2,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"ac\", \"wald\", \"waldcc\", \"score\", \"scorecc\", \"mn\", \"mee\", \"blj\", \"ha\", \"hal\",     \"jp\") )  desctools_binomci(   x,   n,   conf.level = 0.95,   sides = c(\"two.sided\", \"left\", \"right\"),   method = c(\"wilson\", \"wald\", \"waldcc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\",     \"wilsoncc\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\",     \"pratt\", \"midp\", \"lik\", \"blaker\"),   rand = 123,   tol = 1e-05 )"},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"conf.level (proportion) confidence level, defaults 0.95. sides (string) side confidence interval compute. Must one \"two-sided\" (default), \"left\", \"right\". method (string) method use. Can one : \"wald\", \"wilson\", \"wilsoncc\", \"agresti-coull\", \"jeffreys\", \"modified wilson\", \"modified jeffreys\", \"clopper-pearson\", \"arcsine\", \"logit\", \"witting\", \"pratt\", \"midp\", \"lik\", \"blaker\". x (integer(1)) number successes. n (integer(1)) number trials.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"matrix 3 values: est: estimate proportion difference. lwr.ci: estimate lower end confidence interval. upr.ci: estimate upper end confidence interval. matrix 3 columns containing: est: estimate proportion difference. lwr.ci: lower end confidence interval. upr.ci: upper end confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/desctools_binom.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Confidence intervals for a difference of binomials — desctools_binom","text":"desctools_binom(): Several confidence intervals difference proportions. desctools_binomci(): Compute confidence intervals binomial proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.frame object to ggplot object — df2gg","title":"Convert data.frame object to ggplot object — df2gg","text":"Given data.frame object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"df2gg(   df,   colwidths = NULL,   font_size = 10,   col_labels = TRUE,   col_lab_fontface = \"bold\",   hline = TRUE,   bg_fill = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.frame object to ggplot object — df2gg","text":"df (data.frame) data frame. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column df position. NULL, column widths calculated according maximum number characters per column. font_size (numeric(1)) font size. col_labels (flag) whether column names (labels) df used first row output table. col_lab_fontface (string) font face apply first row (column labels col_labels = TRUE). Defaults \"bold\". hline (flag) whether horizontal line printed first row table. bg_fill (string) table background fill color.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.frame object to ggplot object — df2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert data.frame object to ggplot object — df2gg","text":"","code":"if (FALSE) { # \\dontrun{ df2gg(head(iris, 5))  df2gg(head(iris, 5), font_size = 15, colwidths = c(1, 1, 1, 1, 1)) } # }"},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Encode categorical missing values in a data frame — df_explicit_na","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"helper function encode missing entries across groups categorical variables data frame.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"df_explicit_na(   data,   omit_columns = NULL,   char_as_factor = TRUE,   logical_as_factor = FALSE,   na_level = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data (data.frame) data set. omit_columns (character) names variables data modified function. char_as_factor (flag) whether convert character variables data factors. logical_as_factor (flag) whether convert logical variables data factors. na_level (string) string used replace NA empty values inside non-omit_columns columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"data.frame chosen modifications applied.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"Missing entries NA empty strings replaced specified value. factor variables include missing values, missing value inserted last level. Similarly, case character logical variables converted factors char_as_factor logical_as_factor options, missing values set last level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/df_explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Encode categorical missing values in a data frame — df_explicit_na","text":"","code":"my_data <- data.frame(   u = c(TRUE, FALSE, NA, TRUE),   v = factor(c(\"A\", NA, NA, NA), levels = c(\"Z\", \"A\")),   w = c(\"A\", \"B\", NA, \"C\"),   x = c(\"D\", \"E\", \"F\", NA),   y = c(\"G\", \"H\", \"I\", \"\"),   z = c(1, 2, 3, 4),   stringsAsFactors = FALSE )  # Example 1 # Encode missing values in all character or factor columns. df_explicit_na(my_data) #>       u         v         w         x         y z #> 1  TRUE         A         A         D         G 1 #> 2 FALSE <Missing>         B         E         H 2 #> 3    NA <Missing> <Missing>         F         I 3 #> 4  TRUE <Missing>         C <Missing> <Missing> 4 # Also convert logical columns to factor columns. df_explicit_na(my_data, logical_as_factor = TRUE) #>           u         v         w         x         y z #> 1      TRUE         A         A         D         G 1 #> 2     FALSE <Missing>         B         E         H 2 #> 3 <Missing> <Missing> <Missing>         F         I 3 #> 4      TRUE <Missing>         C <Missing> <Missing> 4 # Encode missing values in a subset of columns. df_explicit_na(my_data, omit_columns = c(\"x\", \"y\")) #>       u         v         w    x y z #> 1  TRUE         A         A    D G 1 #> 2 FALSE <Missing>         B    E H 2 #> 3    NA <Missing> <Missing>    F I 3 #> 4  TRUE <Missing>         C <NA>   4  # Example 2 # Here we purposefully convert all `M` values to `NA` in the `SEX` variable. # After running `df_explicit_na` the `NA` values are encoded as `<Missing>` but they are not # included when generating `rtables`. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl)  # If you want the `Na` values to be displayed in the table use the `na_level` argument. adsl <- tern_ex_adsl adsl$SEX[adsl$SEX == \"M\"] <- NA adsl <- df_explicit_na(adsl, na_level = \"Missing Values\")  # Example 3 # Numeric variables that have missing values are not altered. This means that any `NA` value in # a numeric variable will not be included in the summary statistics, nor will they be included # in the denominator value for calculating the percent values. adsl <- tern_ex_adsl adsl$AGE[adsl$AGE < 30] <- NA adsl <- df_explicit_na(adsl)"},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to check if a float value is equal to another float value — .is_equal_float","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"Uses .Machine$double.eps tolerance comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"","code":".is_equal_float(x, y)"},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"x (numeric(1)) float number. y (numeric(1)) float number.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/dot-is_equal_float.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to check if a float value is equal to another float value — .is_equal_float","text":"TRUE identical, otherwise FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Draw grob — draw_grob","title":"Draw grob — draw_grob","text":"Draw grob device page.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Draw grob — draw_grob","text":"","code":"draw_grob(grob, newpage = TRUE, vp = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Draw grob — draw_grob","text":"grob (grob) grid object. newpage (flag) draw new page. vp (viewport NULL) viewport() object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Draw grob — draw_grob","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/draw_grob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Draw grob — draw_grob","text":"","code":"library(dplyr) library(grid)  # \\donttest{ rect <- rectGrob(width = grid::unit(0.5, \"npc\"), height = grid::unit(0.5, \"npc\")) rect %>% draw_grob(vp = grid::viewport(angle = 45))   num <- lapply(1:10, textGrob) num %>%   arrange_grobs(grobs = .) %>%   draw_grob() #> Warning: `stack_grobs()` was deprecated in tern 0.9.4. #> ℹ `tern` plotting functions no longer generate `grob` objects. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>. showViewport()  # }"},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Return an empty numeric if all elements are NA. — empty_vector_if_na","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"Return empty numeric elements NA.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"empty_vector_if_na(x)"},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"x (numeric) vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"empty numeric elements x NA, otherwise x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/empty_vector_if_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Return an empty numeric if all elements are NA. — empty_vector_if_na","text":"","code":"x <- c(NA, NA, NA) # Internal function - empty_vector_if_na"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":null,"dir":"Reference","previous_headings":"","what":"Hazard ratio estimation in interactions — estimate_coef","title":"Hazard ratio estimation in interactions — estimate_coef","text":"function estimates hazard ratios arms interaction variable given specific values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"estimate_coef(   variable,   given,   lvl_var,   lvl_given,   coef,   mmat,   vcov,   conf_level = 0.95 )"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hazard ratio estimation in interactions — estimate_coef","text":"variable, given (character(2)) names two variables interaction. seek estimation levels variable given levels given. lvl_var, lvl_given (character) corresponding levels given levels(). coef (numeric) vector estimated coefficients. mmat (named numeric) vector filled 0s used template obtain design matrix. vcov (matrix) variance-covariance matrix underlying model. conf_level (proportion) confidence level estimate intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hazard ratio estimation in interactions — estimate_coef","text":"list matrices (one per level variable) rows corresponding combinations variable given, columns: coef_hat: Estimation coefficient. coef_se: Standard error estimation. hr: Hazard ratio. lcl, ucl: Lower/upper confidence limit hazard ratio.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hazard ratio estimation in interactions — estimate_coef","text":"Given cox regression investigating effect Arm (, B, C; reference ) Sex (F, M; reference Female). model abbreviated: y ~ Arm + Sex + Arm x Sex. cox regression estimates coefficients along variance-covariance matrix : b1 (arm b), b2 (arm c) b3 (sex m) b4 (arm b: sex m), b5 (arm c: sex m) Given want estimation Hazard Ratio arm C/sex M, estimation given reference arm /Sex M exp(b2 + b3 + b5)/ exp(b3) = exp(b2 + b5), therefore interaction coefficient given b2 + b5 standard error obtained $1.96 * sqrt(Var b2 + Var b5 + 2 * covariance (b2,b5))$ confidence level 0.95.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_coef.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hazard ratio estimation in interactions — estimate_coef","text":"","code":"library(dplyr) library(survival)  ADSL <- tern_ex_adsl %>%   filter(SEX %in% c(\"F\", \"M\"))  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"PFS\") adtte$ARMCD <- droplevels(adtte$ARMCD) adtte$SEX <- droplevels(adtte$SEX)  mod <- coxph(   formula = Surv(time = AVAL, event = 1 - CNSR) ~ (SEX + ARMCD)^2,   data = adtte )  mmat <- stats::model.matrix(mod)[1, ] mmat[!mmat == 0] <- 0"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"analyze & summarize function estimate_multinomial_response() creates layout element estimate proportion proportion confidence interval level factor variable. primary analysis variable, var, factor variable, values used labels within output table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"estimate_multinomial_response(   lyt,   var,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = var,   .stats = \"prop_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_length_proportion(x, .N_col, ...)  a_length_proportion(x, .N_col, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. x (numeric) vector numbers want analyze. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_length_proportion() table layout. s_length_proportion() returns statistics s_proportion(). a_length_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"estimate_multinomial_response(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze() rtables::summarize_row_groups(). s_length_proportion(): Statistics function feeds length x number successes, .N_col total number successes failures s_proportion(). a_length_proportion(): Formatted analysis function used afun estimate_multinomial_response().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_multinomial_rsp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimate proportions of each level of a variable — estimate_multinomial_rsp","text":"","code":"library(dplyr)  # Use of the layout creating function. dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = factor(rep(LETTERS[1:3], each = 4)),   AVAL    = c(A = c(1, 1, 1, 1), B = c(0, 0, 1, 1), C = c(0, 0, 0, 0)) ) %>% mutate(   AVALC = factor(AVAL,     levels = c(0, 1),     labels = c(\"Complete Response (CR)\", \"Partial Response (PR)\")   ) )  lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_multinomial_response(var = \"AVALC\")  tbl <- build_table(lyt, dta_test)  tbl #>                                           A                B                 C        #> ————————————————————————————————————————————————————————————————————————————————————— #> Complete Response (CR)                0 (0.0%)         2 (50.0%)        4 (100.0%)    #>   95% CI (Wald, with correction)    (0.00, 12.50)    (0.00, 100.00)   (87.50, 100.00) #> Partial Response (PR)                4 (100.0%)        2 (50.0%)         0 (0.0%)     #>   95% CI (Wald, with correction)   (87.50, 100.00)   (0.00, 100.00)    (0.00, 12.50)   s_length_proportion(rep(\"CR\", 10), .N_col = 100) #> $n_prop #> [1] 10.0  0.1 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  3.620108 16.379892 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>  s_length_proportion(factor(character(0)), .N_col = 100) #> $n_prop #> [1] 0 0 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1] 0.0 0.5 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   a_length_proportion(rep(\"CR\", 10), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop     10 (10.0%)          0                     Responders #> 2  prop_ci  (3.62, 16.38)          0 95% CI (Wald, with correction) a_length_proportion(factor(character(0)), .N_col = 100) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                      row_label #> 1   n_prop       0 (0.0%)          0                     Responders #> 2  prop_ci   (0.00, 0.50)          0 95% CI (Wald, with correction)"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion estimation — estimate_proportion","title":"Proportion estimation — estimate_proportion","text":"analyze function estimate_proportion() creates layout element estimate proportion responders within studied population. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use constructing confidence interval proportion. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion estimation — estimate_proportion","text":"","code":"estimate_proportion(   lyt,   vars,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )  a_proportion(   df,   .var,   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"clopper-pearson\", \"wilson\", \"wilsonc\", \"strat_wilson\",     \"strat_wilsonc\", \"agresti-coull\", \"jeffreys\"),   weights = NULL,   max_iterations = 50,   variables = list(strata = NULL),   long = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion estimation — estimate_proportion","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . conf_level (proportion) confidence level interval. method (string) method used construct confidence interval proportion successful outcomes; one waldcc, wald, clopper-pearson, wilson, wilsonc, strat_wilson, strat_wilsonc, agresti-coull jeffreys. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights. variables (named list string) list additional analysis variables. long (flag) whether long description required. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n_prop', 'prop_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (logical data.frame) logical vector used, indicates whether subject responder . TRUE represents successful outcome. data.frame provided, also strata variable names must provided variables list element strata strings. case data.frame, logical vector responses must indicated variable name .var. .var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion() table layout. s_proportion() returns statistics n_prop (n proportion) prop_ci (proportion CI) given variable. a_proportion() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion estimation — estimate_proportion","text":"estimate_proportion(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion(): Statistics function estimating proportion along confidence interval. a_proportion(): Formatted analysis function used afun estimate_proportion().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/estimate_proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion estimation — estimate_proportion","text":"","code":"dta_test <- data.frame(   USUBJID = paste0(\"S\", 1:12),   ARM     = rep(LETTERS[1:3], each = 4),   AVAL    = rep(LETTERS[1:3], each = 4) )  basic_table() %>%   split_cols_by(\"ARM\") %>%   estimate_proportion(vars = \"AVAL\") %>%   build_table(df = dta_test) #>                                      A           B           C     #> —————————————————————————————————————————————————————————————————— #> Responders                       <Missing>   <Missing>   <Missing> #> 95% CI (Wald, with correction)   <Missing>   <Missing>   <Missing>  # Case with only logical vector. rsp_v <- c(1, 0, 1, 0, 1, 1, 0, 0) s_proportion(rsp_v) #> $n_prop #> [1] 4.0 0.5 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #> [1]  9.102404 90.897596 #> attr(,\"label\") #> [1] \"95% CI (Wald, with correction)\" #>   # Example for Stratified Wilson CI nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  s_proportion(   df = dta,   .var = \"rsp\",   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"strat_wilson\" ) #> $n_prop #> [1] 49.00  0.49 #> attr(,\"label\") #> [1] \"Responders\" #>  #> $prop_ci #>    lower    upper  #> 40.80675 56.65017  #> attr(,\"label\") #> [1] \"90% CI (Stratified Wilson, without correction)\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Simulated CDISC data for examples — ex_data","title":"Simulated CDISC data for examples — ex_data","text":"Simulated CDISC data examples","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simulated CDISC data for examples — ex_data","text":"","code":"tern_ex_adsl  tern_ex_adae  tern_ex_adlb  tern_ex_adpp  tern_ex_adrs  tern_ex_adtte"},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Simulated CDISC data for examples — ex_data","text":"rds (data.frame) object class tbl_df (inherits tbl, data.frame) 200 rows 21 columns. object class tbl_df (inherits tbl, data.frame) 541 rows 42 columns. object class tbl_df (inherits tbl, data.frame) 4200 rows 50 columns. object class tbl_df (inherits tbl, data.frame) 522 rows 25 columns. object class tbl_df (inherits tbl, data.frame) 1600 rows 29 columns. object class tbl_df (inherits tbl, data.frame) 1000 rows 28 columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ex_data.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Simulated CDISC data for examples — ex_data","text":"tern_ex_adsl: ADSL data tern_ex_adae: ADAE data tern_ex_adlb: ADLB data tern_ex_adpp: ADPP data tern_ex_adrs: ADRS data tern_ex_adtte: ADTTE data","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Missing data — explicit_na","title":"Missing data — explicit_na","text":"Substitute missing data string factor level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Missing data — explicit_na","text":"","code":"explicit_na(x, label = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Missing data — explicit_na","text":"x (factor character) values missing values substituted. label (string) string missing data replaced .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Missing data — explicit_na","text":"x NA values substituted label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/explicit_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Missing data — explicit_na","text":"","code":"explicit_na(c(NA, \"a\", \"b\")) #> [1] \"<Missing>\" \"a\"         \"b\"         is.na(explicit_na(c(NA, \"a\", \"b\"))) #> [1] FALSE FALSE FALSE  explicit_na(factor(c(NA, \"a\", \"b\"))) #> [1] <Missing> a         b         #> Levels: a b <Missing> is.na(explicit_na(factor(c(NA, \"a\", \"b\")))) #> [1] FALSE FALSE FALSE  explicit_na(sas_na(c(\"a\", \"\"))) #> [1] \"a\"         \"<Missing>\""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract elements by name — extract_by_name","title":"Extract elements by name — extract_by_name","text":"utility function extracts elements vector x names. Differences standard [ function :","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract elements by name — extract_by_name","text":"","code":"extract_by_name(x, names)"},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract elements by name — extract_by_name","text":"x (named vector) extract named elements . names (character) vector names extract.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract elements by name — extract_by_name","text":"NULL x NULL, otherwise extracted elements x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_by_name.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract elements by name — extract_by_name","text":"x NULL, still always NULL returned (base function). x NULL, intersection names made names elements returned. , names appear x returned NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"Prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates, subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"extract_rsp_biomarkers(   variables,   data,   groups_lists = list(),   control = control_logistic(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (named list) controls response definition confidence level produced control_logistic(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_rsp, prop, , lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"can also specify continuous variable rsp use response_definition control convert internally logical variable reflecting binary response.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_biomarkers.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare response data estimates for multiple biomarkers in a single data frame — extract_rsp_biomarkers","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\")  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in logistic regression models with one covariate `RACE`. The subgroups # are defined by the levels of `BMRKR2`. df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp      prop        or #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.8200000 0.9755036 #> 2       AGE                          Age   200   164 0.8200000 0.9952416 #> 3    BMRKR1 Continuous Level Biomarker 1    70    53 0.7571429 1.1524547 #> 4       AGE                          Age    70    53 0.7571429 0.9261012 #> 5    BMRKR1 Continuous Level Biomarker 1    68    58 0.8529412 0.8773122 #> 6       AGE                          Age    68    58 0.8529412 0.9867104 #> 7    BMRKR1 Continuous Level Biomarker 1    62    53 0.8548387 0.8792921 #> 8       AGE                          Age    62    53 0.8548387 1.0630262 #>         lcl      ucl conf_level      pval     pval_label     subgroup    var #> 1 0.8804862 1.080775       0.95 0.6352602 p-value (Wald) All Patients    ALL #> 2 0.9462617 1.046757       0.95 0.8530389 p-value (Wald) All Patients    ALL #> 3 0.9462127 1.403650       0.95 0.1584187 p-value (Wald)          LOW BMRKR2 #> 4 0.8487519 1.010500       0.95 0.0844837 p-value (Wald)          LOW BMRKR2 #> 5 0.7277189 1.057657       0.95 0.1699778 p-value (Wald)       MEDIUM BMRKR2 #> 6 0.8798911 1.106498       0.95 0.8189816 p-value (Wald)       MEDIUM BMRKR2 #> 7 0.7189748 1.075357       0.95 0.2103709 p-value (Wald)         HIGH BMRKR2 #> 8 0.9595973 1.177603       0.95 0.2418840 p-value (Wald)         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually, and we add a stratification # variable `STRATA1`. We also here use a continuous variable `EOSDY` # which is then binarized internally (response is defined as this variable # being larger than 750). df_grouped <- extract_rsp_biomarkers(   variables = list(     rsp = \"EOSDY\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\",     strata = \"STRATA1\"   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ),   control = control_logistic(     response_definition = \"I(response > 750)\"   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_rsp prop or lcl ucl conf_level #> 1    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 2       AGE                          Age   200     0    0 NA  NA  NA       0.95 #> 3    BMRKR1 Continuous Level Biomarker 1    70     0    0 NA  NA  NA       0.95 #> 4       AGE                          Age    70     0    0 NA  NA  NA       0.95 #> 5    BMRKR1 Continuous Level Biomarker 1   138     0    0 NA  NA  NA       0.95 #> 6       AGE                          Age   138     0    0 NA  NA  NA       0.95 #> 7    BMRKR1 Continuous Level Biomarker 1   200     0    0 NA  NA  NA       0.95 #> 8       AGE                          Age   200     0    0 NA  NA  NA       0.95 #>   pval     pval_label        subgroup    var                    var_label #> 1   NA p-value (Wald)    All Patients    ALL                 All Patients #> 2   NA p-value (Wald)    All Patients    ALL                 All Patients #> 3   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 4   NA p-value (Wald)             low BMRKR2 Continuous Level Biomarker 2 #> 5   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6   NA p-value (Wald)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 7   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #> 8   NA p-value (Wald) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2  content #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #> 7 analysis #> 8 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"Prepares response rates odds ratios population subgroups data frames. Simple wrapper h_odds_ratio_subgroups_df() h_proportion_subgroups_df(). Result list two data.frames: prop . variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"","code":"extract_rsp_subgroups(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_rsp_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare response data for population subgroups in data frames — extract_rsp_subgroups","text":"named list two elements: prop: data.frame containing columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. : data.frame containing columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers across population subgroups single data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables), optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"","code":"extract_survival_biomarkers(   variables,   data,   groups_lists = list(),   control = control_coxreg(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_biomarkers.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data estimates for multiple biomarkers in a single data frame — extract_survival_biomarkers","text":"data.frame columns biomarker, biomarker_label, n_tot, n_tot_events, median, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"Prepares estimates median survival times treatment hazard ratios population subgroups data frames. Simple wrapper h_survtime_subgroups_df() h_coxph_subgroups_df(). Result list two data.frames: survtime hr. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"","code":"extract_survival_subgroups(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. label_all (string) label total population analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extract_survival_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare survival data for population subgroups in data frames — extract_survival_subgroups","text":"named list two elements: survtime: data.frame containing columns arm, n, n_events, median, subgroup, var, var_label, row_type. hr: data.frame containing columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values — extreme_format","title":"Format extreme values — extreme_format","text":"rtables formatting functions handle extreme values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(digits = 2L)  h_format_threshold(x, digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values — extreme_format","text":"digits (integer(1)) number decimal places display. x (numeric(1)) value format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values — extreme_format","text":"h_get_format_threshold() returns list 2 elements: threshold, low high thresholds, format_string, thresholds formatted strings. h_format_threshold() returns given value, value within digit threshold relation given value digit threshold, formatted string.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format extreme values — extreme_format","text":"input, apply format specified number digits. value threshold, returns \"<0.01\" e.g. number digits 2. value threshold, returns \">999.99\" e.g. number digits 2. zero, returns \"0.00\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Format extreme values — extreme_format","text":"h_get_format_threshold(): Internal helper function calculate threshold create formatted strings used Formatting Functions. Returns list elements threshold format_string. h_format_threshold(): Internal helper function apply threshold format value. Creates formatted string used Formatting Functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/extreme_format.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values — extreme_format","text":"","code":"h_get_format_threshold(2L) #> $threshold #>    low   high  #>   0.01 999.99  #>  #> $format_string #>       low      high  #>   \"<0.01\" \">999.99\"  #>   h_format_threshold(0.001) #> [1] \"<0.01\" h_format_threshold(1000) #> [1] \">999.99\""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for confidence interval — f_conf_level","text":"","code":"f_conf_level(conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for confidence interval — f_conf_level","text":"conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/f_conf_level.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for confidence interval — f_conf_level","text":"string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to create label for p-value — f_pval","text":"","code":"f_pval(test_mean)"},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to create label for p-value — f_pval","text":"test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/f_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to create label for p-value — f_pval","text":"string.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse factor levels and keep only those new group levels — fct_collapse_only","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"collapses levels keeps new group levels, order provided. returned factor levels order given, possible missing level last (included missing values).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(.f, ..., .na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":".f (factor character) original vector. ... (named character) levels vector provided collapsed new level given respective name. .na_level (string) level use levels, missing new factor. Note level must contained new levels specified ....","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"modified factor collapsed levels. Values levels included given character vector input set missing level .na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"existing NAs input vector replaced missing level. needed, explicit_na() can called separately result.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fct_collapse_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Collapse factor levels and keep only those new group levels — fct_collapse_only","text":"","code":"fct_collapse_only(factor(c(\"a\", \"b\", \"c\", \"d\")), TRT = \"b\", CTRL = c(\"c\", \"d\")) #> [1] <Missing> TRT       CTRL      CTRL      #> Levels: TRT CTRL <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":null,"dir":"Reference","previous_headings":"","what":"Discard specified levels of a factor — fct_discard","title":"Discard specified levels of a factor — fct_discard","text":"discards observations well levels specified factor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(x, discard)"},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Discard specified levels of a factor — fct_discard","text":"x (factor) original factor. discard (character) levels discard.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Discard specified levels of a factor — fct_discard","text":"modified factor observations well levels discard dropped.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_discard.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Discard specified levels of a factor — fct_discard","text":"","code":"fct_discard(factor(c(\"a\", \"b\", \"c\")), \"c\") #> [1] a b #> Levels: a b"},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":null,"dir":"Reference","previous_headings":"","what":"Insertion of explicit missing values in a factor — fct_explicit_na_if","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"inserts explicit missing values factor based condition. Additionally, existing NA values explicitly converted given na_level.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(x, condition, na_level = \"<Missing>\")"},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"x (factor) original factor. condition (logical) positions insert missing values. na_level (string) level use missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"modified factor inserted existing NA converted na_level.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fct_explicit_na_if.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Insertion of explicit missing values in a factor — fct_explicit_na_if","text":"","code":"fct_explicit_na_if(factor(c(\"a\", \"b\", NA)), c(TRUE, FALSE, FALSE)) #> [1] <Missing> b         <Missing> #> Levels: a b <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":null,"dir":"Reference","previous_headings":"","what":"Fitting functions for Cox proportional hazards regression — fit_coxreg","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"Fitting functions univariate multivariate Cox regression models.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"fit_coxreg_univar(variables, data, at = list(), control = control_coxreg())  fit_coxreg_multivar(variables, data, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"variables (named list) names variables found data, passed named list corresponding time, event, arm, strata, covariates terms. arm missing variables, Cox model(s) including covariates fitted corresponding effect estimates tabulated later. data (data.frame) dataset containing variables fit models. (list numeric) candidate covariate numeric, use specify value covariate effect estimated. control (list) list parameters returned helper function control_coxreg().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar() returns coxreg.univar class object named list 5 elements: mod: Cox regression models fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model. : Value covariate effect estimated. fit_coxreg_multivar() returns coxreg.multivar class object named list 4 elements: mod: Cox regression model fitted survival::coxph(). data: original data frame input. control: original control input. vars: variables used model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"fit_coxreg_univar(): Fit series univariate Cox regression models given inputs. fit_coxreg_multivar(): Fit multivariate Cox regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"using fit_coxreg_univar two study arms.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fitting functions for Cox proportional hazards regression — fit_coxreg","text":"","code":"library(survival)  set.seed(1, kind = \"Mersenne-Twister\")  # Testing dataset [survival::bladder]. dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  plot(   survfit(Surv(time, status) ~ armcd + covar1, data = dta_bladder),   lty = 2:4,   xlab = \"Months\",   col = c(\"blue1\", \"blue2\", \"blue3\", \"blue4\", \"red1\", \"red2\", \"red3\", \"red4\") )   # fit_coxreg_univar  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  ## Cox regression: arm + 1 covariate, stratified analysis. mod3 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", strata = \"covar2\",     covariates = c(\"covar1\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: no arm, only covariates. mod4 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # fit_coxreg_multivar  ## Cox regression: multivariate Cox regression. multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )  # Example without treatment arm. multivar_covs_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit for logistic regression — fit_logistic","title":"Fit for logistic regression — fit_logistic","text":"Fit (conditional) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit for logistic regression — fit_logistic","text":"","code":"fit_logistic(   data,   variables = list(response = \"Response\", arm = \"ARMCD\", covariates = NULL, interaction =     NULL, strata = NULL),   response_definition = \"response\" )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit for logistic regression — fit_logistic","text":"data (data.frame) data frame model fit. variables (named list string) list additional analysis variables. response_definition (string) definition event terms response. used fitting (conditional) logistic regression model left hand side formula.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit for logistic regression — fit_logistic","text":"fitted logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"model-specification","dir":"Reference","previous_headings":"","what":"Model Specification","title":"Fit for logistic regression — fit_logistic","text":"variables list needs include following elements: arm: Treatment arm variable name. response: response arm variable name. Usually 0/1 variable. covariates: either NULL (covariates) character vector covariate variable names. interaction: either NULL (interaction) string single covariate variable name already included covariates. interaction treatment arm included model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit for logistic regression — fit_logistic","text":"","code":"library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred"},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"fits Subgroup Treatment Effect Pattern logistic regression models binary (response) outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated odds ratios comparison second level vs. first one. (conditional) logistic regression model fit : response ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"fit_rsp_step(variables, data, control = c(control_step(), control_logistic()))"},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"variables (named list character) list analysis variables: needs response, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_logistic().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_rsp_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for binary (response) outcome — fit_rsp_step","text":"","code":"# Testing dataset with just two treatment arms. library(survival) library(dplyr)  adrs_f <- tern_ex_adrs %>%   filter(     PARAMCD == \"BESRSPI\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to have Placebo as reference arm for Odds Ratio calculations.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     RSP = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     SEX = factor(SEX)   )  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. # We use a large enough bandwidth to avoid too small subgroups and linear separation in those. step_matrix <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = 0.9)) ) dim(step_matrix) #> [1] 39 11 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.925        1.472755 #> [2,]             0.050                0            0.950        2.028546 #> [3,]             0.075                0            0.975        2.204086 #> [4,]             0.100                0            1.000        2.799776 #> [5,]             0.125                0            1.000        2.969998 #> [6,]             0.150                0            1.000        3.149068 #>      Interval Lower Interval Upper   n    logor       se   ci_lower ci_upper #> [1,]      0.4459546       11.74529 131 1.835008 1.134560 -0.3886885 4.058703 #> [2,]      0.4459546       12.73387 134 1.895158 1.136248 -0.3318481 4.122163 #> [3,]      0.4459546       14.75099 138 1.947699 1.136969 -0.2807193 4.176116 #> [4,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [5,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258 #> [6,]      0.4459546       18.49236 142 1.931001 1.135866 -0.2952561 4.157258  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different logistic regression options, including confidence level. step_matrix2 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(conf_level = 0.9), control_step(bandwidth = NULL, degree = 1)) )  # Use a global constant model. This is helpful as a reference for the subgroup models. step_matrix3 <- fit_rsp_step(   variables = variables,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL, num_points = 2L)) )  # It is also possible to use strata, i.e. use conditional logistic regression models. variables2 <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = \"AGE\",   response = \"RSP\",   strata = c(\"STRATA1\", \"STRATA2\") )  step_matrix4 <- fit_rsp_step(   variables = variables2,   data = adrs_f,   control = c(control_logistic(), control_step(bandwidth = NULL)) )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"fits subgroup treatment effect pattern (STEP) models survival outcome. treatment arm variable must exactly 2 levels, first one taken reference estimated hazard ratios comparison second level vs. first one. model fit : Surv(time, event) ~ arm * poly(biomarker, degree) + covariates + strata(strata) degree specified control_step().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"fit_survival_step(   variables,   data,   control = c(control_step(), control_coxph()) )"},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"variables (named list character) list analysis variables: needs time, event, arm, biomarker, optional covariates strata. data (data.frame) dataset containing variables summarize. control (named list) combined control list control_step() control_coxph().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"matrix class step. first part columns describe subgroup intervals used biomarker variable, including center intervals bounds. second part columns contain estimates treatment arm comparison.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"default degree 0 biomarker variable included model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/fit_survival_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subgroup treatment effect pattern (STEP) fit for survival outcome — fit_survival_step","text":"","code":"# Testing dataset with just two treatment arms. library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = \"Treatment Arm\", \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  variables <- list(   arm = \"ARM\",   biomarker = \"BMRKR1\",   covariates = c(\"AGE\", \"BMRKR2\"),   event = \"is_event\",   time = \"AVAL\" )  # Fit default STEP models: Here a constant treatment effect is estimated in each subgroup. step_matrix <- fit_survival_step(   variables = variables,   data = adtte_f ) dim(step_matrix) #> [1] 39 12 head(step_matrix) #>      Percentile Center Percentile Lower Percentile Upper Interval Center #> [1,]             0.025                0            0.275        1.472755 #> [2,]             0.050                0            0.300        2.028546 #> [3,]             0.075                0            0.325        2.204086 #> [4,]             0.100                0            0.350        2.799776 #> [5,]             0.125                0            0.375        2.969998 #> [6,]             0.150                0            0.400        3.149068 #>      Interval Lower Interval Upper  n events      loghr        se   ci_lower #> [1,]      0.4459546       4.182444 39     29 0.03729601 0.4243013 -0.7943192 #> [2,]      0.4459546       4.349471 43     31 0.23246622 0.3881347 -0.5282639 #> [3,]      0.4459546       4.626913 46     32 0.07952492 0.3813113 -0.6678314 #> [4,]      0.4459546       4.805767 50     35 0.09020455 0.3638368 -0.6229026 #> [5,]      0.4459546       4.929816 53     37 0.15522702 0.3477999 -0.5264483 #> [6,]      0.4459546       5.020539 57     41 0.11135760 0.3332843 -0.5418676 #>       ci_upper #> [1,] 0.8689112 #> [2,] 0.9931963 #> [3,] 0.8268813 #> [4,] 0.8033117 #> [5,] 0.8369023 #> [6,] 0.7645828  # Specify different polynomial degree for the biomarker interaction to use more flexible local # models. Or specify different Cox regression options. step_matrix2 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(conf_level = 0.9), control_step(degree = 2)) )  # Use a global model with cubic interaction and only 5 points. step_matrix3 <- fit_survival_step(   variables = variables,   data = adtte_f,   control = c(control_coxph(), control_step(bandwidth = NULL, degree = 3, num_points = 5L)) )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"forest_viewport(   tbl,   width_row_names = NULL,   width_columns = NULL,   width_forest = grid::unit(1, \"null\"),   gap_column = grid::unit(1, \"lines\"),   gap_header = grid::unit(1, \"lines\"),   mat_form = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a viewport tree for the forest plot — forest_viewport","text":"tbl (VTableTree)rtables table object. width_row_names (grid::unit) width row names. width_columns (grid::unit) width column spans. width_forest (grid::unit) width forest plot. gap_column (grid::unit) gap width columns. gap_header (grid::unit) gap width header. mat_form (MatrixPrintForm) matrix print form table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a viewport tree for the forest plot — forest_viewport","text":"viewport tree.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/forest_viewport.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a viewport tree for the forest plot — forest_viewport","text":"","code":"library(grid)  tbl <- rtable(   header = rheader(     rrow(\"\", \"E\", rcell(\"CI\", colspan = 2)),     rrow(\"\", \"A\", \"B\", \"C\")   ),   rrow(\"row 1\", 1, 0.8, 1.1),   rrow(\"row 2\", 1.4, 0.8, 1.6),   rrow(\"row 3\", 1.2, 0.8, 1.2) )  # \\donttest{ v <- forest_viewport(tbl) #> Warning: `forest_viewport()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> Warning: `vp_forest_table_part()` was deprecated in tern 0.9.4. #> ℹ `g_forest` now generates `ggplot` objects. This function is no longer used #>   within `tern`. #> ℹ The deprecated feature was likely used in the tern package. #>   Please report the issue at #>   <https://github.com/insightsengineering/tern/issues>.  grid::grid.newpage() showViewport(v)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":null,"dir":"Reference","previous_headings":"","what":"Format automatically using data significant digits — format_auto","title":"Format automatically using data significant digits — format_auto","text":"Formatting function majority default methods used analyze_vars(). non-derived values, significant digits data used (e.g. range), derived values one digits (measure location dispersion like mean, standard deviation). function can called internally \"auto\" like, example, .formats = c(\"mean\" = \"auto\"). See details see works inner function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format automatically using data significant digits — format_auto","text":"","code":"format_auto(dt_var, x_stat)"},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format automatically using data significant digits — format_auto","text":"dt_var (numeric) variable data statistics calculated . Used find significant digits. analyze_vars comes .df_row (see rtables::additional_fun_params), row data row splits. column split considered. x_stat (string) string indicating current statistical method used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format automatically using data significant digits — format_auto","text":"string rtables prints table cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Format automatically using data significant digits — format_auto","text":"internal function needed work rtables default structure format functions, .e. function(x, ...), x results statistical evaluation. can one element (e.g. .stats = \"mean_sd\").","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_auto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format automatically using data significant digits — format_auto","text":"","code":"x_todo <- c(0.001, 0.2, 0.0011000, 3, 4) res <- c(mean(x_todo[1:3]), sd(x_todo[1:3]))  # x is the result coming into the formatting function -> res!! format_auto(dt_var = x_todo, x_stat = \"mean_sd\")(x = res) #> [1] \"0.06737 (0.11486)\" format_auto(x_todo, \"range\")(x = range(x_todo)) #> [1] \"0.0010 - 4.0000\" no_sc_x <- c(0.0000001, 1) format_auto(no_sc_x, \"range\")(x = no_sc_x) #> [1] \"0.0000001 - 1.0000000\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction — format_count_fraction","title":"Format count and fraction — format_count_fraction","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction — format_count_fraction","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction — format_count_fraction","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction — format_count_fraction","text":"","code":"format_count_fraction(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"Formats count together fraction special consideration count 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"string format count (fraction %). count 0, format 0.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and percentage with fixed single decimal place — format_count_fraction_fixed_dp","text":"","code":"format_count_fraction_fixed_dp(x = c(2, 0.6667)) #> [1] \"2 (66.7%)\" format_count_fraction_fixed_dp(x = c(2, 0.5)) #> [1] \"2 (50.0%)\" format_count_fraction_fixed_dp(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":null,"dir":"Reference","previous_headings":"","what":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"Formats count together fraction special consideration count less 10.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"x (numeric(2)) vector length 2 count fraction, respectively. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"string format count (fraction %). count less 10, count printed.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_count_fraction_lt10.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format count and fraction with special case for count < 10 — format_count_fraction_lt10","text":"","code":"format_count_fraction_lt10(x = c(275, 0.9673)) #> [1] \"275 (96.7%)\" format_count_fraction_lt10(x = c(2, 0.6667)) #> [1] \"2\" format_count_fraction_lt10(x = c(9, 1)) #> [1] \"9\""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Format a single extreme value — format_extreme_values","title":"Format a single extreme value — format_extreme_values","text":"Create formatting function single extreme value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_extreme_values(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format a single extreme value — format_extreme_values","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format a single extreme value — format_extreme_values","text":"rtables formatting function uses threshold digits return formatted extreme value.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format a single extreme value — format_extreme_values","text":"","code":"format_fun <- format_extreme_values(2L) format_fun(x = 0.127) #> [1] \"0.13\" format_fun(x = Inf) #> [1] \">999.99\" format_fun(x = 0) #> [1] \"0.00\" format_fun(x = 0.009) #> [1] \"<0.01\""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Format extreme values part of a confidence interval — format_extreme_values_ci","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"Formatting Function extreme values part confidence interval. Values formatted e.g. \"(xx.xx, xx.xx)\" number digits 2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_extreme_values_ci(digits = 2L)"},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"digits (integer(1)) number decimal places display.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"rtables formatting function uses threshold digits return formatted extreme values confidence interval.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_extreme_values_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format extreme values part of a confidence interval — format_extreme_values_ci","text":"","code":"format_fun <- format_extreme_values_ci(2L) format_fun(x = c(0.127, Inf)) #> [1] \"(0.13, >999.99)\" format_fun(x = c(0, 0.009)) #> [1] \"(0.00, <0.01)\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage — format_fraction","title":"Format fraction and percentage — format_fraction","text":"Formats fraction together ratio percent.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage — format_fraction","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage — format_fraction","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage — format_fraction","text":"","code":"format_fraction(x = c(num = 2L, denom = 3L)) #> [1] \"2/3 (66.7%)\" format_fraction(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"Formats fraction together ratio percent fixed single decimal place. Includes trailing zero case whole number percentages always keep one decimal place.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"x (named integer) vector elements num denom. ... used. Required rtables interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"string format num / denom (ratio %). num 0, format num / denom.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_fixed_dp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction and percentage with fixed single decimal place — format_fraction_fixed_dp","text":"","code":"format_fraction_fixed_dp(x = c(num = 1L, denom = 2L)) #> [1] \"1/2 (50.0%)\" format_fraction_fixed_dp(x = c(num = 1L, denom = 4L)) #> [1] \"1/4 (25.0%)\" format_fraction_fixed_dp(x = c(num = 0L, denom = 3L)) #> [1] \"0/3\""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":null,"dir":"Reference","previous_headings":"","what":"Format fraction with lower threshold — format_fraction_threshold","title":"Format fraction with lower threshold — format_fraction_threshold","text":"Formats fraction second element input x fraction. applies lower threshold, just stated fraction smaller .","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fraction_threshold(threshold)"},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format fraction with lower threshold — format_fraction_threshold","text":"threshold (proportion) lower threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format fraction with lower threshold — format_fraction_threshold","text":"rtables formatting function takes numeric input x second element fraction formatted. fraction equal threshold, displayed percentage. positive threshold, returns, e.g. \"<1\" threshold 0.01. zero, just \"0\" returned.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_fraction_threshold.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format fraction with lower threshold — format_fraction_threshold","text":"","code":"format_fun <- format_fraction_threshold(0.05) format_fun(x = c(20, 0.1)) #> [1] 10 format_fun(x = c(2, 0.01)) #> [1] \"<5\" format_fun(x = c(0, 0)) #> [1] \"0\""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":null,"dir":"Reference","previous_headings":"","what":"Format numeric values by significant figures — format_sigfig","title":"Format numeric values by significant figures — format_sigfig","text":"Format numeric values print specified number significant figures.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"format_sigfig(sigfig, format = \"xx\", num_fmt = \"fg\")"},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format numeric values by significant figures — format_sigfig","text":"sigfig (integer(1)) number significant figures display. format (string) format label (string) apply printing value. Decimal places string ignored favor formatting significant figures. Formats options : \"xx\", \"xx / xx\", \"(xx, xx)\", \"xx - xx\", \"xx (xx)\". num_fmt (string) numeric format modifiers apply value. Defaults \"fg\" standard significant figures formatting - fixed (non-scientific notation) format (\"f\") sigfig equal number significant figures instead decimal places (\"g\"). See formatC() format argument options.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format numeric values by significant figures — format_sigfig","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_sigfig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format numeric values by significant figures — format_sigfig","text":"","code":"fmt_3sf <- format_sigfig(3) fmt_3sf(1.658) #> [1] \"1.66\" fmt_3sf(1e1) #> [1] \"10.0\"  fmt_5sf <- format_sigfig(5) fmt_5sf(0.57) #> [1] \"0.57000\" fmt_5sf(0.000025645) #> [1] \"0.000025645\""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":null,"dir":"Reference","previous_headings":"","what":"Format XX as a formatting function — format_xx","title":"Format XX as a formatting function — format_xx","text":"Translate string x dots interpreted number place holders, others formatting elements.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format XX as a formatting function — format_xx","text":"","code":"format_xx(str)"},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format XX as a formatting function — format_xx","text":"str (string) template.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format XX as a formatting function — format_xx","text":"rtables formatting function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/format_xx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format XX as a formatting function — format_xx","text":"","code":"test <- list(c(1.658, 0.5761), c(1e1, 785.6))  z <- format_xx(\"xx (xx.x)\") sapply(test, z) #> [1] \"2 (0.6)\"    \"10 (785.6)\"  z <- format_xx(\"xx.x - xx.x\") sapply(test, z) #> [1] \"1.7 - 0.6\"  \"10 - 785.6\"  z <- format_xx(\"xx.x, incl. xx.x% NE\") sapply(test, z) #> [1] \"1.7, incl. 0.6% NE\"  \"10, incl. 785.6% NE\""},{"path":"https://insightsengineering.github.io/tern/reference/formatting_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Formatting functions — formatting_functions","title":"Formatting functions — formatting_functions","text":"See list formatting functions created tern work rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/formatting_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Formatting functions — formatting_functions","text":"available formats can listed via formatters::list_valid_format_labels(). Additional custom formats can created via formatters::sprintf_format() function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman plot — g_bland_altman","title":"Bland-Altman plot — g_bland_altman","text":"Graphing function produces Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman plot — g_bland_altman","text":"","code":"g_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman plot — g_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman plot — g_bland_altman","text":"ggplot Bland-Altman plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman plot — g_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  g_bland_altman(x = x, y = y, conf_level = 0.9)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a forest plot from an rtable — g_forest","text":"","code":"g_forest(   tbl,   col_x = attr(tbl, \"col_x\"),   col_ci = attr(tbl, \"col_ci\"),   vline = 1,   forest_header = attr(tbl, \"forest_header\"),   xlim = c(0.1, 10),   logx = TRUE,   x_at = c(0.1, 1, 10),   width_row_names = lifecycle::deprecated(),   width_columns = NULL,   width_forest = lifecycle::deprecated(),   lbl_col_padding = 0,   rel_width_forest = 0.25,   font_size = 12,   col_symbol_size = attr(tbl, \"col_symbol_size\"),   col = getOption(\"ggplot2.discrete.colour\")[1],   ggtheme = NULL,   as_list = FALSE,   gp = lifecycle::deprecated(),   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a forest plot from an rtable — g_forest","text":"tbl (VTableTree)rtables table least one column single value one column 2 values. col_x (integer(1) NULL) column index estimator. default tries get tbl attribute col_x, otherwise needs manually specified. NULL, points excluded forest plot. col_ci (integer(1) NULL) column index confidence intervals. default tries get tbl attribute col_ci, otherwise needs manually specified. NULL, lines excluded forest plot. vline (numeric(1) NULL) x coordinate vertical line, NULL line omitted. forest_header (character(2)) text displayed left right vline, respectively. vline = NULL forest_header printed. default tries get tbl attribute forest_header. NULL, defaults extracted table possible, set \"Comparison\\nBetter\" \"Treatment\\nBetter\" . xlim (numeric(2)) limits x axis. logx (flag) show x-values logarithm scale. x_at (numeric) x-tick locations, NULL, x_at set vline xlim values. width_row_names Please use lbl_col_padding argument instead. width_columns (numeric) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. width_forest Please use rel_width_forest argument instead. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0. rel_width_forest (proportion) proportion total width allocate forest plot. Relative width table 1 - rel_width_forest. as_list = TRUE, parameter ignored. font_size (numeric(1)) font size. col_symbol_size (numeric NULL) column index tbl containing data used determine relative size estimator plot symbol. Typically, symbol size proportional sample size used calculate estimator. NULL, symbol size used subgroups. default tries get tbl attribute col_symbol_size, otherwise needs manually specified. col (character) color(s). ggtheme (theme) graphical theme provided ggplot2 control styling plot. as_list (flag) whether two ggplot objects returned list. TRUE, named list two elements, table plot, returned. FALSE (default) table forest plot printed side--side via cowplot::plot_grid(). gp g_forest now generated ggplot object. argument longer used. draw g_forest now generated ggplot object. argument longer used. newpage g_forest now generated ggplot object. argument longer used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a forest plot from an rtable — g_forest","text":"ggplot forest plot table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a forest plot from an rtable — g_forest","text":"Given rtables::rtable() object least one column single value one column 2 values, converts table ggplot2::ggplot() object generates accompanying forest plot. table forest plot printed side--side.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_forest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a forest plot from an rtable — g_forest","text":"","code":"library(dplyr) library(forcats) library(nestcolor)  adrs <- tern_ex_adrs n_records <- 20 adrs_labels <- formatters::var_labels(adrs, fill = TRUE) adrs <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   slice(seq_len(n_records)) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs) <- c(adrs_labels, \"Response\") df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"STRATA2\")),   data = adrs ) # Full commonly used response table.  tbl <- basic_table() %>%   tabulate_rsp_subgroups(df) g_forest(tbl)   # Odds ratio only table.  tbl_or <- basic_table() %>%   tabulate_rsp_subgroups(df, vars = c(\"n_tot\", \"or\", \"ci\")) g_forest(   tbl_or,   forest_header = c(\"Comparison\\nBetter\", \"Treatment\\nBetter\") )   # Survival forest plot example. adtte <- tern_ex_adtte # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = TRUE) adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- list(   \"ARM\" = adtte_labels[\"ARM\"],   \"SEX\" = adtte_labels[\"SEX\"],   \"AVALU\" = adtte_labels[\"AVALU\"],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- as.character(labels) df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) table_hr <- basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) g_forest(table_hr)   # Works with any `rtable`. tbl <- rtable(   header = c(\"E\", \"CI\", \"N\"),   rrow(\"\", 1, c(.8, 1.2), 200),   rrow(\"\", 1.2, c(1.1, 1.4), 50) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   col_symbol_size = 3 )   tbl <- rtable(   header = rheader(     rrow(\"\", rcell(\"A\", colspan = 2)),     rrow(\"\", \"c1\", \"c2\")   ),   rrow(\"row 1\", 1, c(.8, 1.2)),   rrow(\"row 2\", 1.2, c(1.1, 1.4)) ) g_forest(   tbl = tbl,   col_x = 1,   col_ci = 2,   xlim = c(0.5, 2),   x_at = c(0.5, 1, 2),   vline = 1,   forest_header = c(\"Hello\", \"World\") )"},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Individual patient plots — g_ipp","title":"Individual patient plots — g_ipp","text":"Line plot(s) displaying trend patients' parameter values time rendered. Patients' individual baseline values can added plot(s) reference.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Individual patient plots — g_ipp","text":"","code":"g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var = \"USUBJID\",   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   plotting_choices = c(\"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\"),   max_obs_per_plot = 4,   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Individual patient plots — g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. plotting_choices (string) specifies options displaying plots. Must one \"all_in_one\", \"split_by_max_obs\", \"separate_by_obs\". max_obs_per_plot (integer(1)) number observations plotted one plot. Ignored plotting_choices \"separate_by_obs\". col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Individual patient plots — g_ipp","text":"ggplot object list ggplot objects.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Individual patient plots — g_ipp","text":"g_ipp(): Plotting function individual patient plots , depending user preference, renders single graphic compiles list graphics show trends individual's parameter values time.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Individual patient plots — g_ipp","text":"","code":"library(dplyr) library(nestcolor)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  plot_list <- g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   ylab = \"SGOT/ALT (U/L)\",   title = \"Individual Patient Plots\",   add_baseline_hline = TRUE,   plotting_choices = \"split_by_max_obs\",   max_obs_per_plot = 5 ) plot_list #> [[1]]  #>  #> [[2]]  #>"},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Kaplan-Meier plot — g_km","title":"Kaplan-Meier plot — g_km","text":"survival model, graphic rendered along tabulated annotation including number patient risk given time median survival per group.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kaplan-Meier plot — g_km","text":"","code":"g_km(   df,   variables,   control_surv = control_surv_timepoint(),   col = NULL,   lty = NULL,   lwd = 0.5,   censor_show = TRUE,   pch = 3,   size = 2,   max_time = NULL,   xticks = NULL,   xlab = \"Days\",   yval = c(\"Survival\", \"Failure\"),   ylab = paste(yval, \"Probability\"),   ylim = NULL,   title = NULL,   footnotes = NULL,   font_size = 10,   ci_ribbon = FALSE,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE,   annot_surv_med = TRUE,   annot_coxph = FALSE,   annot_stats = NULL,   annot_stats_vlines = FALSE,   control_coxph_pw = control_coxph(),   ref_group_coxph = NULL,   control_annot_surv_med = control_surv_med_annot(),   control_annot_coxph = control_coxph_annot(),   legend_pos = NULL,   rel_height_plot = 0.75,   ggtheme = NULL,   as_list = FALSE,   draw = lifecycle::deprecated(),   newpage = lifecycle::deprecated(),   gp = lifecycle::deprecated(),   vp = lifecycle::deprecated(),   name = lifecycle::deprecated(),   annot_coxph_ref_lbls = lifecycle::deprecated(),   position_coxph = lifecycle::deprecated(),   position_surv_med = lifecycle::deprecated(),   width_annots = lifecycle::deprecated() )"},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kaplan-Meier plot — g_km","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. control_surv (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string)\"plain\" (default), \"log\", \"log-log\" confidence interval type, see survival::survfit(). Note option \"none\" longer supported. col (character) lines colors. Length vector equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). censor_show (flag) whether show censored observations. pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. xlab (string) x-axis label. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. font_size (numeric(1)) font size use text. ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE. annot_surv_med (flag) compute add annotation table Kaplan-Meier curve estimating median survival time per group. annot_coxph (flag) whether add annotation table survival::coxph() model. annot_stats (string NULL) statistics annotations add plot. Options median (median survival follow-time) min (minimum survival follow-time). annot_stats_vlines (flag) add vertical lines corresponding statistics specified annot_stats. annot_stats NULL lines added. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_annot_surv_med (list) parameters control position size annotation table added plot annot_surv_med = TRUE, specified using control_surv_med_annot() function. Parameter options : x, y, w, h, fill. See control_surv_med_annot() details. control_annot_coxph (list) parameters control position size annotation table added plot annot_coxph = TRUE, specified using control_coxph_annot() function. Parameter options : x, y, w, h, fill, ref_lbls. See control_coxph_annot() details. legend_pos (numeric(2) NULL) vector containing x- y-coordinates, respectively, legend position relative KM plot area. NULL (default), legend positioned bottom right corner plot, middle right plot needed prevent overlapping. rel_height_plot (proportion) proportion total figure height allocate Kaplan-Meier plot. Relative height patients risk table 1 - rel_height_plot. annot_at_risk = FALSE as_list = TRUE, parameter ignored. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot. as_list (flag) whether two ggplot objects returned list annot_at_risk = TRUE. TRUE, named list two elements, plot table, returned. FALSE (default) patients risk table printed plot via cowplot::plot_grid(). draw function longer generates grob objects. newpage function longer generates grob objects. gp function longer generates grob objects. vp function longer generates grob objects. name function longer generates grob objects. annot_coxph_ref_lbls Please use ref_lbls element control_annot_coxph instead. position_coxph Please use x y elements control_annot_coxph instead. position_surv_med Please use x y elements control_annot_surv_med instead. width_annots Please use w element control_annot_surv_med (surv_med) control_annot_coxph (coxph).\"","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Kaplan-Meier plot — g_km","text":"ggplot Kaplan-Meier plot (optionally) summary table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kaplan-Meier plot — g_km","text":"","code":"library(dplyr) library(nestcolor)  df <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) variables <- list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\")  # Basic examples g_km(df = df, variables = variables)  g_km(df = df, variables = variables, yval = \"Failure\")   # Examples with customization parameters applied g_km(   df = df,   variables = variables,   control_surv = control_surv_timepoint(conf_level = 0.9),   col = c(\"grey25\", \"grey50\", \"grey75\"),   annot_at_risk_title = FALSE,   lty = 1:3,   font_size = 8 )  g_km(   df = df,   variables = variables,   annot_stats = c(\"min\", \"median\"),   annot_stats_vlines = TRUE,   max_time = 3000,   ggtheme = ggplot2::theme_minimal() )   # Example with pairwise Cox-PH analysis annotation table, adjusted annotation tables g_km(   df = df, variables = variables,   annot_coxph = TRUE,   control_coxph = control_coxph(pval_method = \"wald\", ties = \"exact\", conf_level = 0.99),   control_annot_coxph = control_coxph_annot(x = 0.26, w = 0.35),   control_annot_surv_med = control_surv_med_annot(x = 0.8, y = 0.9, w = 0.35) )"},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Line plot with optional table — g_lineplot","title":"Line plot with optional table — g_lineplot","text":"Line plot optional table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Line plot with optional table — g_lineplot","text":"","code":"g_lineplot(   df,   alt_counts_df = NULL,   variables = control_lineplot_vars(),   mid = \"mean\",   interval = \"mean_ci\",   whiskers = c(\"mean_ci_lwr\", \"mean_ci_upr\"),   table = NULL,   sfun = s_summary,   ...,   mid_type = \"pl\",   mid_point_size = 2,   position = ggplot2::position_dodge(width = 0.4),   legend_title = NULL,   legend_position = \"bottom\",   ggtheme = nestcolor::theme_nest(),   xticks = NULL,   xlim = NULL,   ylim = NULL,   x_lab = obj_label(df[[variables[[\"x\"]]]]),   y_lab = NULL,   y_lab_add_paramcd = TRUE,   y_lab_add_unit = TRUE,   title = \"Plot of Mean and 95% Confidence Limits by Visit\",   subtitle = \"\",   subtitle_add_paramcd = TRUE,   subtitle_add_unit = TRUE,   caption = NULL,   table_format = NULL,   table_labels = NULL,   table_font_size = 3,   errorbar_width = 0.45,   newpage = lifecycle::deprecated(),   col = NULL,   linetype = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Line plot with optional table — g_lineplot","text":"df (data.frame) data set containing analysis variables. alt_counts_df (data.frame NULL) data set used () counts objects groups stratification. variables (named character) vector variable names df include: x (string) name x-axis variable. y (string) name y-axis variable. group_var (string NULL) name grouping variable (strata), .e. treatment arm. Can NA indicate lack groups. subject_var (string NULL) name subject variable. applies group_var NULL. paramcd (string NA) name variable parameter's code. Used y-axis label plot's subtitle. Can NA paramcd added y-axis label subtitle. y_unit (string NA) name variable units y. Used y-axis label plot's subtitle. Can NA y unit added y-axis label subtitle. facet_var (string NA) name secondary grouping variable used plot faceting, .e. treatment arm. Can NA indicate lack groups. mid (character NULL) names statistics plotted midpoints. statistics indicated mid variable must present object returned sfun, double numeric type vector length one. interval (character NULL) names statistics plotted intervals. statistics indicated interval variable must present object returned sfun, double numeric type vector length two. Set interval = NULL intervals added plot. whiskers (character) names interval whiskers plotted. Names must match names list element interval returned sfun (e.g. mean_ci_lwr element sfun(x)[[\"mean_ci\"]]). possible specify one whisker , suppress whiskers setting interval = NULL. table (character NULL) names statistics displayed table plot. statistics indicated table variable must present object returned sfun. sfun (function) function compute values required statistics. must return named list atomic vectors. names list elements refer names statistics used mid, interval, table. must able accept input vector data statistics computed. ... optional arguments sfun. mid_type (string) controls type mid plot, can point (\"p\"), line (\"l\"), point line (\"pl\"). mid_point_size (numeric(1)) font size mid plot points. position (character call) geom element position adjustment, either string, result call position adjustment function. legend_title (string) legend title. legend_position (string) position plot legend (\"none\", \"left\", \"right\", \"bottom\", \"top\", two-element numeric vector). ggtheme (theme) graphical theme provided ggplot2 control styling plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis, use variables$x numeric. NULL (default), labeling::extended() used determine optimal tick positions x-axis. variables$x numeric, argument ignored. xlim (numeric(2)) vector containing lower upper limits x-axis, respectively. NULL (default), default scale range used. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. x_lab (string NULL) x-axis label. NULL label added. y_lab (string NULL) y-axis label. NULL label added. y_lab_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added y-axis label (y_lab). y_lab_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added y-axis label (y_lab). title (string) plot title. subtitle (string) plot subtitle. subtitle_add_paramcd (flag) whether paramcd, .e. unique(df[[variables[\"paramcd\"]]]) added plot's subtitle (subtitle). subtitle_add_unit (flag) whether y-axis unit, .e. unique(df[[variables[\"y_unit\"]]]) added plot's subtitle (subtitle). caption (string) optional caption plot. table_format (named character NULL) format patterns descriptive statistics used (optional) table appended plot. passed directly h_format_row function format parameter. Names table_format must match names statistics returned sfun function. table_labels (named character NULL) labels descriptive statistics used (optional) table appended plot. Names table_labels must match names statistics returned sfun function. table_font_size (numeric(1)) font size text table. errorbar_width (numeric(1)) width error bars. newpage used. col (character) color(s). See ?ggplot2::aes_colour_fill_alpha example values. linetype (character) line type(s). See ?ggplot2::aes_linetype_size_shape example values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Line plot with optional table — g_lineplot","text":"ggplot line plot (statistics table applicable).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_lineplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Line plot with optional table — g_lineplot","text":"","code":"library(nestcolor)  adsl <- tern_ex_adsl adlb <- tern_ex_adlb %>% dplyr::filter(ANL01FL == \"Y\", PARAMCD == \"ALT\", AVISIT != \"SCREENING\") adlb$AVISIT <- droplevels(adlb$AVISIT) adlb <- dplyr::mutate(adlb, AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min))  # Mean with CI g_lineplot(adlb, adsl, subtitle = \"Laboratory Test:\")   # Mean with CI, no stratification with group_var g_lineplot(adlb, variables = control_lineplot_vars(group_var = NA))   # Mean, upper whisker of CI, no group_var(strata) counts N g_lineplot(   adlb,   whiskers = \"mean_ci_upr\",   title = \"Plot of Mean and Upper 95% Confidence Limit by Visit\" )   # Median with CI g_lineplot(   adlb,   adsl,   mid = \"median\",   interval = \"median_ci\",   whiskers = c(\"median_ci_lwr\", \"median_ci_upr\"),   title = \"Plot of Median and 95% Confidence Limits by Visit\" )   # Mean, +/- SD g_lineplot(adlb, adsl,   interval = \"mean_sdi\",   whiskers = c(\"mean_sdi_lwr\", \"mean_sdi_upr\"),   title = \"Plot of Median +/- SD by Visit\" )   # Mean with CI plot with stats table g_lineplot(adlb, adsl, table = c(\"n\", \"mean\", \"mean_ci\"))   # Mean with CI, table and customized confidence level g_lineplot(   adlb,   adsl,   table = c(\"n\", \"mean\", \"mean_ci\"),   control = control_analyze_vars(conf_level = 0.80),   title = \"Plot of Mean and 80% Confidence Limits by Visit\" )   # Mean with CI, table, filtered data adlb_f <- dplyr::filter(adlb, ARMCD != \"ARM A\" | AVISIT == \"BASELINE\") g_lineplot(adlb_f, table = c(\"n\", \"mean\"))"},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a STEP graph — g_step","title":"Create a STEP graph — g_step","text":"Based STEP results, creates ggplot graph showing estimated HR along continuous biomarker value subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a STEP graph — g_step","text":"","code":"g_step(   df,   use_percentile = \"Percentile Center\" %in% names(df),   est = list(col = \"blue\", lty = 1),   ci_ribbon = list(fill = getOption(\"ggplot2.discrete.colour\")[1], alpha = 0.5),   col = getOption(\"ggplot2.discrete.colour\") )"},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a STEP graph — g_step","text":"df (tibble) result tidy.step(). use_percentile (flag) whether use percentiles x axis actual biomarker values. est (named list)col lty settings estimate line. ci_ribbon (named list NULL)fill alpha settings confidence interval ribbon area, NULL plot CI ribbon. col (character) color(s).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a STEP graph — g_step","text":"ggplot STEP graph.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/g_step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a STEP graph — g_step","text":"","code":"library(nestcolor) library(survival) lung$sex <- factor(lung$sex)  # Survival example. vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) step_data <- broom::tidy(step_matrix)  # Default plot. g_step(step_data)   # Add the reference 1 horizontal line. library(ggplot2) g_step(step_data) +   ggplot2::geom_hline(ggplot2::aes(yintercept = 1), linetype = 2)   # Use actual values instead of percentiles, different color for estimate and no CI, # use log scale for y axis. g_step(   step_data,   use_percentile = FALSE,   est = list(col = \"blue\", lty = 1),   ci_ribbon = NULL ) + scale_y_log10()   # Adding another curve based on additional column. step_data$extra <- exp(step_data$`Percentile Center`) g_step(step_data) +   ggplot2::geom_line(ggplot2::aes(y = extra), linetype = 2, color = \"green\")   # Response example. vars <- list(   response = \"status\",   arm = \"sex\",   biomarker = \"age\" )  step_matrix <- fit_rsp_step(   variables = vars,   data = lung,   control = c(     control_logistic(response_definition = \"I(response == 2)\"),     control_step()   ) ) step_data <- broom::tidy(step_matrix) g_step(step_data)"},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":null,"dir":"Reference","previous_headings":"","what":"Horizontal waterfall plot — g_waterfall","title":"Horizontal waterfall plot — g_waterfall","text":"basic waterfall plot visualizes quantity height ordered value markup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"g_waterfall(   height,   id,   col_var = NULL,   col = getOption(\"ggplot2.discrete.colour\"),   xlab = NULL,   ylab = NULL,   col_legend_title = NULL,   title = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Horizontal waterfall plot — g_waterfall","text":"height (numeric) vector containing values plotted waterfall bars. id (character) vector containing identifiers use x-axis label waterfall bars. col_var (factor, character, NULL) categorical variable bar coloring. NULL default. col (character) color(s). xlab (string) x label. Default \"ID\". ylab (string) y label. Default \"Value\". col_legend_title (string) text displayed legend title. title (string) text displayed plot title.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Horizontal waterfall plot — g_waterfall","text":"ggplot waterfall plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/g_waterfall.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Horizontal waterfall plot — g_waterfall","text":"","code":"library(dplyr) library(nestcolor)  g_waterfall(height = c(3, 5, -1), id = letters[1:3])   g_waterfall(   height = c(3, 5, -1),   id = letters[1:3],   col_var = letters[1:3] )   adsl_f <- tern_ex_adsl %>%   select(USUBJID, STUDYID, ARM, ARMCD, SEX)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"OVRINV\") %>%   mutate(pchg = rnorm(n(), 10, 50))  adrs_f <- head(adrs_f, 30) adrs_f <- adrs_f[!duplicated(adrs_f$USUBJID), ] head(adrs_f) #> # A tibble: 5 × 30 #>   STUDYID COUNTRY SITEID SUBJID   AGE SEX   ARMCD ARM      ACTARMCD ACTARM RACE  #>   <chr>   <fct>   <chr>  <chr>  <dbl> <fct> <fct> <fct>    <fct>    <fct>  <fct> #> 1 AB12345 BRA     BRA-1  id-105  37.8 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> 2 AB12345 BRA     BRA-1  id-171  29.8 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 3 AB12345 BRA     BRA-1  id-177  38.9 F     ARM B B: Plac… ARM B    B: Pl… ASIAN #> 4 AB12345 BRA     BRA-1  id-23   41.3 F     ARM A A: Drug… ARM A    A: Dr… AMER… #> 5 AB12345 BRA     BRA-1  id-59   26.7 F     ARM A A: Drug… ARM A    A: Dr… ASIAN #> # ℹ 19 more variables: TRTSDTM <dttm>, TRTEDTM <dttm>, EOSDY <dbl>, #> #   STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, REGION1 <fct>, #> #   SAFFL <fct>, USUBJID <chr>, AVISIT <fct>, PARAMCD <fct>, PARAM <fct>, #> #   AVALC <fct>, AVAL <int>, ADTM <date>, AVISITN <dbl>, DTHFL <fct>, #> #   pchg <dbl>  g_waterfall(   height = adrs_f$pchg,   id = adrs_f$USUBJID,   col_var = adrs_f$AVALC )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   col_var = adrs_f$SEX )   g_waterfall(   height = adrs_f$pchg,   id = paste(\"asdfdsfdsfsd\", adrs_f$USUBJID),   xlab = \"ID\",   ylab = \"Percentage Change\",   title = \"Waterfall plot\" )"},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to return a named list of covariate names — get_covariates","title":"Utility function to return a named list of covariate names — get_covariates","text":"Utility function return named list covariate names","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to return a named list of covariate names — get_covariates","text":"","code":"get_covariates(covariates)"},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to return a named list of covariate names — get_covariates","text":"covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_covariates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to return a named list of covariate names — get_covariates","text":"named list character vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":null,"dir":"Reference","previous_headings":"","what":"Smooth function with optional grouping — get_smooths","title":"Smooth function with optional grouping — get_smooths","text":"produces loess smoothed estimates y Student confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Smooth function with optional grouping — get_smooths","text":"","code":"get_smooths(df, x, y, groups = NULL, level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Smooth function with optional grouping — get_smooths","text":"df (data.frame) data set containing analysis variables. x (string) x column name. y (string) y column name. groups (character NULL) vector optional grouping variables names. level (proportion) level confidence interval use (0.95 default).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/get_smooths.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Smooth function with optional grouping — get_smooths","text":"data.frame original x, smoothed y, ylow, yhigh, optional groups variables formatted factor type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert list of groups to a data frame — groups_list_to_df","title":"Convert list of groups to a data frame — groups_list_to_df","text":"converts list group levels data frame format expected rtables::add_combo_levels().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"groups_list_to_df(groups_list)"},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert list of groups to a data frame — groups_list_to_df","text":"groups_list (named list character) specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert list of groups to a data frame — groups_list_to_df","text":"tibble required format.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/groups_list_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert list of groups to a data frame — groups_list_to_df","text":"","code":"grade_groups <- list(   \"Any Grade (%)\" = c(\"1\", \"2\", \"3\", \"4\", \"5\"),   \"Grade 3-4 (%)\" = c(\"3\", \"4\"),   \"Grade 5 (%)\" = \"5\" ) groups_list_to_df(grade_groups) #> # A tibble: 3 × 4 #>   valname  label         levelcombo exargs     #>   <chr>    <chr>         <list>     <list>     #> 1 AnyGrade Any Grade (%) <chr [5]>  <list [0]> #> 2 Grade34  Grade 3-4 (%) <chr [2]>  <list [0]> #> 3 Grade5   Grade 5 (%)   <chr [1]>  <list [0]>"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"Helper function prepare ADLB data frame used input count_abnormal_by_worst_grade(). following pre-processing steps applied: adlb filtered variable avisit include post-baseline visits. adlb filtered variables worst_flag_low worst_flag_high worst grades (either direction) included. standard lab grade variable atoxgr, following two variables derived added adlb: grade direction variable (e.g. GRADE_DIR). variable takes value \"HIGH\" atoxgr > 0, \"LOW\" atoxgr < 0, \"ZERO\" otherwise. toxicity grade variable (e.g. GRADE_ANL) negative values atoxgr replaced absolute values. Unused factor levels dropped adlb via droplevels().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(   adlb,   atoxgr = \"ATOXGR\",   avisit = \"AVISIT\",   worst_flag_low = \"WGRLOFL\",   worst_flag_high = \"WGRHIFL\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"adlb (data.frame) ADLB data frame. atoxgr (string) name analysis toxicity grade variable. must factor variable. avisit (string) name analysis visit variable. worst_flag_low (string) name worst low lab grade flag variable. variable set \"Y\" indicating records worst low lab grades. worst_flag_high (string) name worst high lab grade flag variable. variable set \"Y\" indicating records worst high lab grades.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"h_adlb_abnormal_by_worst_grade() returns adlb data frame two new variables: GRADE_DIR GRADE_ANL.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_abnormal_by_worst_grade.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB for count_abnormal_by_worst_grade() — h_adlb_abnormal_by_worst_grade","text":"","code":"h_adlb_abnormal_by_worst_grade(tern_ex_adlb) %>%   dplyr::select(ATOXGR, GRADE_DIR, GRADE_ANL) %>%   head(10) #> # A tibble: 10 × 3 #>    ATOXGR GRADE_DIR GRADE_ANL #>    <fct>  <fct>     <fct>     #>  1 -3     LOW       3         #>  2 0      ZERO      0         #>  3 0      ZERO      0         #>  4 2      HIGH      2         #>  5 0      ZERO      0         #>  6 0      ZERO      0         #>  7 -4     LOW       4         #>  8 1      HIGH      1         #>  9 -1     LOW       1         #> 10 0      ZERO      0"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"Helper function prepare df generate patient count shift table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"h_adlb_worsen(   adlb,   worst_flag_low = NULL,   worst_flag_high = NULL,   direction_var )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"adlb (data.frame) ADLB data frame. worst_flag_low (named vector) worst low post-baseline lab grade flag variable. See implemented following examples. worst_flag_high (named vector) worst high post-baseline lab grade flag variable. See implemented following examples. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"h_adlb_worsen() returns adlb data.frame containing worst labs specified according worst_flag_low worst_flag_high direction specified according direction_var. instance, lab needed low direction , records flagged worst_flag_low selected. lab needed low high directions, worst low records selected low direction, worst high record selected high direction.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_adlb_worsen.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare ADLB with worst labs — h_adlb_worsen","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"Helper function merges ADSL ADLB datasets missing lab test records inserted output dataset. Remember na_level must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"h_adsl_adlb_merge_using_worst_flag(   adsl,   adlb,   worst_flag = c(WGRHIFL = \"Y\"),   by_visit = FALSE,   no_fillin_visits = c(\"SCREENING\", \"BASELINE\") )"},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"adsl (data.frame) ADSL data frame. adlb (data.frame) ADLB data frame. worst_flag (named character) worst post-baseline lab flag variable. See implemented following examples. by_visit (flag) defaults FALSE generate worst grade per patient. worst grade per patient per visit specified worst_flag, by_visit TRUE generate worst grade patient per visit. no_fillin_visits (named character) visits considered post-baseline worst toxicity grade. Defaults c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"df containing variables shared adlb adsl along variables PARAM, PARAMCD, ATOXGR, BTOXGR relevant analysis. Optionally, AVISIT AVISITN included by_visit = TRUE no_fillin_visits = c(\"SCREENING\", \"BASELINE\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"result data missing records created following situations: Patients present adsl lab data adlb (baseline post-baseline). Patients post-baseline lab values. Patients without post-baseline values flagged worst.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_adsl_adlb_merge_using_worst_flag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for deriving analysis datasets for select laboratory tables — h_adsl_adlb_merge_using_worst_flag","text":"","code":"# `h_adsl_adlb_merge_using_worst_flag` adlb_out <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRHIFL\" = \"Y\") )  # `h_adsl_adlb_merge_using_worst_flag` by visit example adlb_out_by_visit <- h_adsl_adlb_merge_using_worst_flag(   tern_ex_adsl,   tern_ex_adlb,   worst_flag = c(\"WGRLOVFL\" = \"Y\"),   by_visit = TRUE )"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(.var, .df_row, variables, interaction_item = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to return results of a linear model — h_ancova","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to return results of a linear model — h_ancova","text":"summary linear model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to return results of a linear model — h_ancova","text":"","code":"h_ancova(   .var = \"Sepal.Length\",   .df_row = iris,   variables = list(arm = \"Species\", covariates = c(\"Petal.Length * Petal.Width\", \"Sepal.Width\")) ) #>  Species    emmean     SE  df lower.CL upper.CL #>  setosa       6.15 0.3370 143     5.49     6.82 #>  versicolor   5.72 0.0668 143     5.59     5.85 #>  virginica    5.41 0.1490 143     5.11     5.70 #>  #> Confidence level used: 0.95"},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Helper function s_count_occurrences_by_grade() insert grade groupings list individual grade frequencies. order final result follows order grade_groups. elements -grade group (), .e. grade group equal refs moved end. Grade groups names must unique.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   grade_groups,   refs,   remove_single = TRUE,   only_grade_groups = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"grade_groups (named list character) list containing groupings grades. refs (named list numeric) named list name corresponds reference grade level entry represents count. remove_single (flag)TRUE include elements one-element grade groups output list; case grade groups names included output. only_grade_groups set TRUE argument ignored. only_grade_groups (flag) whether specified grade groups included, individual grade rows removed (TRUE), grades grade groups displayed (FALSE).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"Formatted list grade groupings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_append_grade_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_occurrences_by_grade() — h_append_grade_groups","text":"","code":"h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade 1-2` #> [1] 30 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 20 #>  #> $`Grade 3-4` #> [1] 70 #>  #> $`3` #> [1] 30 #>  #> $`4` #> [1] 40 #>  #> $`5` #> [1] 50 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(5:1),     \"Grade A\" = \"5\",     \"Grade B\" = c(\"4\", \"3\")   ),   list(\"1\" = 10, \"2\" = 20, \"3\" = 30, \"4\" = 40, \"5\" = 50) ) #> $`Any Grade` #> [1] 150 #>  #> $`Grade A` #> [1] 50 #>  #> $`Grade B` #> [1] 70 #>  #> $`4` #> [1] 40 #>  #> $`3` #> [1] 30 #>  #> $`2` #> [1] 20 #>  #> $`1` #> [1] 10 #>   h_append_grade_groups(   list(     \"Any Grade\" = as.character(1:5),     \"Grade 1-2\" = c(\"1\", \"2\"),     \"Grade 3-4\" = c(\"3\", \"4\")   ),   list(\"1\" = 10, \"2\" = 5, \"3\" = 0) ) #> $`Any Grade` #> [1] 15 #>  #> $`Grade 1-2` #> [1] 15 #>  #> $`1` #> [1] 10 #>  #> $`2` #> [1] 5 #>  #> $`Grade 3-4` #> [1] 0 #>  #> $`3` #> [1] 0 #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain column indices — h_col_indices","title":"Obtain column indices — h_col_indices","text":"Helper function extract column indices VTableTree given vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain column indices — h_col_indices","text":"","code":"h_col_indices(table_tree, col_names)"},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain column indices — h_col_indices","text":"table_tree (VTableTree)rtables table object extract indices . col_names (character) vector column names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_col_indices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain column indices — h_col_indices","text":"vector column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for s_count_cumulative() — h_count_cumulative","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"Helper function calculate count fraction x values lower upper tail given threshold.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"h_count_cumulative(   x,   threshold,   lower_tail = TRUE,   include_eq = TRUE,   na.rm = TRUE,   .N_col )"},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"x (numeric) vector numbers want analyze. threshold (numeric(1)) cutoff value threshold count values x. lower_tail (flag) whether count lower tail, default TRUE. include_eq (flag) whether include value equal threshold count, default TRUE. na.rm (flag) whether NA values removed x prior analysis. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"named vector items: count: count values less , less equal , greater , greater equal threshold user specification. fraction: fraction count.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_count_cumulative.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for s_count_cumulative() — h_count_cumulative","text":"","code":"set.seed(1, kind = \"Mersenne-Twister\") x <- c(sample(1:10, 10), NA) .N_col <- length(x)  h_count_cumulative(x, 5, .N_col = .N_col) #>     count  fraction  #> 5.0000000 0.4545455  h_count_cumulative(x, 5, lower_tail = FALSE, include_eq = FALSE, na.rm = FALSE, .N_col = .N_col) #>     count  fraction  #> 6.0000000 0.5454545  h_count_cumulative(x, 0, lower_tail = FALSE, .N_col = .N_col) #>      count   fraction  #> 10.0000000  0.9090909  h_count_cumulative(x, 100, lower_tail = FALSE, .N_col = .N_col) #>    count fraction  #>        0        0"},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Cox proportional hazards regression — h_cox_regression","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"Helper functions used fit_coxreg_univar() fit_coxreg_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"h_coxreg_univar_formulas(variables, interaction = FALSE)  h_coxreg_multivar_formula(variables)  h_coxreg_univar_extract(effect, covar, data, mod, control = control_coxreg())  h_coxreg_multivar_extract(var, data, mod, control = control_coxreg())"},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"variables (named list string) list additional analysis variables. interaction (flag) TRUE, model includes interaction studied treatment candidate covariate. Note univariate models without treatment arm, multivariate models, interaction can used needs FALSE. effect (string) treatment variable. covar (string) name covariate model. data (data.frame) dataset containing variables summarize. mod (coxph) Cox regression model fitted survival::coxph(). control (list) list controls returned control_coxreg(). var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas() returns character vector coercible formulas (e.g stats::.formula()). h_coxreg_multivar_formula() returns string coercible formula (e.g stats::.formula()). h_coxreg_univar_extract() returns data.frame variables effect, term, term_label, level, n, hr, lcl, ucl, pval. h_coxreg_multivar_extract() returns data.frame variables pval, hr, lcl, ucl, level, n, term, term_label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"h_coxreg_univar_formulas(): Helper Cox regression formula. Creates list formulas. used internally fit_coxreg_univar() comparison univariate Cox regression models. h_coxreg_multivar_formula(): Helper multivariate Cox regression formula. Creates formulas string. used internally fit_coxreg_multivar() comparison multivariate Cox regression models. Interactions included multivariate Cox regression model. h_coxreg_univar_extract(): Utility function help tabulate result univariate Cox regression model. h_coxreg_multivar_extract(): Tabulation multivariate Cox regressions. Utility function help tabulate result multivariate Cox regression model treatment/covariate variable.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_cox_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for Cox proportional hazards regression — h_cox_regression","text":"","code":"# `h_coxreg_univar_formulas`  ## Simple formulas. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\")   ) ) #>                                        ref  #>     \"survival::Surv(time, status) ~ armcd\"  #>                                          X  #> \"survival::Surv(time, status) ~ armcd + X\"  #>                                          y  #> \"survival::Surv(time, status) ~ armcd + y\"   ## Addition of an optional strata. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ) ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd + X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd + y + strata(SITE)\"   ## Inclusion of the interaction term. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\", covariates = c(\"X\", \"y\"),     strata = \"SITE\"   ),   interaction = TRUE ) #>                                                       ref  #>     \"survival::Surv(time, status) ~ armcd + strata(SITE)\"  #>                                                         X  #> \"survival::Surv(time, status) ~ armcd * X + strata(SITE)\"  #>                                                         y  #> \"survival::Surv(time, status) ~ armcd * y + strata(SITE)\"   ## Only covariates fitted in separate models. h_coxreg_univar_formulas(   variables = list(     time = \"time\", event = \"status\", covariates = c(\"X\", \"y\")   ) ) #>                                      X                                      y  #> \"survival::Surv(time, status) ~ 1 + X\" \"survival::Surv(time, status) ~ 1 + y\"   # `h_coxreg_multivar_formula`  h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\")   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE\"  # Addition of an optional strata. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", arm = \"ARMCD\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ ARMCD + RACE + AGE + strata(SITE)\"  # Example without treatment arm. h_coxreg_multivar_formula(   variables = list(     time = \"AVAL\", event = \"event\", covariates = c(\"RACE\", \"AGE\"),     strata = \"SITE\"   ) ) #> [1] \"survival::Surv(AVAL, event) ~ 1 + RACE + AGE + strata(SITE)\"  library(survival)  dta_simple <- data.frame(   time = c(5, 5, 10, 10, 5, 5, 10, 10),   status = c(0, 0, 1, 0, 0, 1, 1, 1),   armcd = factor(LETTERS[c(1, 1, 1, 1, 2, 2, 2, 2)], levels = c(\"A\", \"B\")),   var1 = c(45, 55, 65, 75, 55, 65, 85, 75),   var2 = c(\"F\", \"M\", \"F\", \"M\", \"F\", \"M\", \"F\", \"U\") ) mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_univar_extract(   effect = \"armcd\", covar = \"armcd\", mod = mod, data = dta_simple ) result #>       effect  term       term_label level n       hr       lcl      ucl #> 1 Treatment: armcd B vs control (A)     B 8 6.551448 0.4606904 93.16769 #>       pval #> 1 0.165209  mod <- coxph(Surv(time, status) ~ armcd + var1, data = dta_simple) result <- h_coxreg_multivar_extract(   var = \"var1\", mod = mod, data = dta_simple ) result #>        pval        hr      lcl      ucl level n term term_label #> 2 0.4456195 0.9423284 0.808931 1.097724  var1 8 var1       var1"},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to tidy survival fit data — h_data_plot","title":"Helper function to tidy survival fit data — h_data_plot","text":"Convert survival fit data data frame designed plotting within g_km. starts broom::tidy() result, : Post-processes strata column factor. Extends stratum additional first row time 0 probability 1 downstream plot lines start coordinates. Adds censor column. Filters rows max_time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"h_data_plot(fit_km, armval = \"All\", max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to tidy survival fit data — h_data_plot","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to tidy survival fit data — h_data_plot","text":"tibble columns time, n.risk, n.event, n.censor, estimate, std.error, conf.high, conf.low, strata, censor.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_data_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to tidy survival fit data — h_data_plot","text":"","code":"library(dplyr) library(survival)  # Test with multiple arms tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot() #> # A tibble: 203 × 10 #>     time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>    <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <fct>  #>  1   0       70       0        0    1        0          1        1     ARM A  #>  2  10.4     69       1        0    0.986    0.0146     1        0.958 ARM A  #>  3  20.5     68       1        0    0.971    0.0208     1        0.932 ARM A  #>  4  21.5     67       1        0    0.957    0.0257     1        0.910 ARM A  #>  5  25.3     66       0        1    0.957    0.0257     1        0.910 ARM A  #>  6  48.1     65       1        0    0.942    0.0300     0.999    0.888 ARM A  #>  7  66.6     64       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  8  73.9     63       0        1    0.942    0.0300     0.999    0.888 ARM A  #>  9  78.9     62       0        1    0.942    0.0300     0.999    0.888 ARM A  #> 10  90.3     61       1        0    0.926    0.0342     0.991    0.866 ARM A  #> # ℹ 193 more rows #> # ℹ 1 more variable: censor <dbl>  # Test with single arm tern_ex_adtte %>%   filter(PARAMCD == \"OS\", ARMCD == \"ARM B\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot(armval = \"ARM B\") #> # A tibble: 74 × 10 #>      time n.risk n.event n.censor estimate std.error conf.high conf.low strata #>     <dbl>  <dbl>   <dbl>    <dbl>    <dbl>     <dbl>     <dbl>    <dbl> <chr>  #>  1   0        74       0        0    1        0          1        1     ARM B  #>  2   2.17     73       1        0    0.986    0.0138     1        0.960 ARM B  #>  3  16.9      72       1        0    0.973    0.0196     1        0.936 ARM B  #>  4  22.6      71       1        0    0.959    0.0242     1        0.914 ARM B  #>  5  26.3      70       1        0    0.945    0.0282     0.999    0.894 ARM B  #>  6  57.5      69       1        0    0.932    0.0317     0.991    0.875 ARM B  #>  7  80.0      68       1        0    0.918    0.0350     0.983    0.857 ARM B  #>  8  81.6      67       1        0    0.904    0.0381     0.974    0.839 ARM B  #>  9  88.6      66       1        0    0.890    0.0411     0.965    0.822 ARM B  #> 10 102.       65       1        0    0.877    0.0439     0.955    0.804 ARM B  #> # ℹ 64 more rows #> # ℹ 1 more variable: censor <dbl>"},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":null,"dir":"Reference","previous_headings":"","what":"ggplot decomposition — h_decompose_gg","title":"ggplot decomposition — h_decompose_gg","text":"elements composing ggplot extracted organized list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ggplot decomposition — h_decompose_gg","text":"","code":"h_decompose_gg(gg)"},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"ggplot decomposition — h_decompose_gg","text":"gg (ggplot) graphic decompose.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"ggplot decomposition — h_decompose_gg","text":"named list elements: panel: panel. yaxis: y-axis. xaxis: x-axis. xlab: x-axis label. ylab: y-axis label. guide: legend.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_decompose_gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ggplot decomposition — h_decompose_gg","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   yval = \"Survival\",   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\",   footnotes = \"ff\" ) #> Warning: `h_ggkm()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  g_el <- h_decompose_gg(gg) #> Warning: `h_decompose_gg()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"red\", fill = \"gray85\", lwd = 5)) grid::grid.draw(g_el$panel)   grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"royalblue\", fill = \"gray85\", lwd = 5)) grid::grid.draw(with(g_el, cbind(ylab, yaxis)))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"h_format_row(x, format, labels = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"x (named list) list numerical values formatted optionally labeled. Elements x must numeric vectors. format (named character NULL) format patterns x. Names format must match names x. parameter passed directly rtables::format_rcell function format parameter. labels (named character NULL) optional labels x. Names labels must match names x. label specified element x, function tries use label names (order) attribute element (depending one exists NULL NA NaN). none attributes attached given element x, label automatically generated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"single row data.frame object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_format_row.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to format the optional g_lineplot table — h_format_row","text":"","code":"mean_ci <- c(48, 51) x <- list(mean = 50, mean_ci = mean_ci) format <- c(mean = \"xx.x\", mean_ci = \"(xx.xx, xx.xx)\") labels <- c(mean = \"My Mean\") h_format_row(x, format, labels) #>   My Mean             V1 #> 1    50.0 (48.00, 51.00)  attr(mean_ci, \"label\") <- \"Mean 95% CI\" x <- list(mean = 50, mean_ci = mean_ci) h_format_row(x, format, labels) #>   My Mean    Mean 95% CI #> 1    50.0 (48.00, 51.00)"},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create simple line plot over time — h_g_ipp","title":"Helper function to create simple line plot over time — h_g_ipp","text":"Function generates simple line plot displaying parameter trends time.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"h_g_ipp(   df,   xvar,   yvar,   xlab,   ylab,   id_var,   title = \"Individual Patient Plots\",   subtitle = \"\",   caption = NULL,   add_baseline_hline = FALSE,   yvar_baseline = \"BASE\",   ggtheme = nestcolor::theme_nest(),   col = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create simple line plot over time — h_g_ipp","text":"df (data.frame) data set containing analysis variables. xvar (string) time point variable plotted x-axis. yvar (string) continuous analysis variable plotted y-axis. xlab (string) plot label x-axis. ylab (string) plot label y-axis. id_var (string) variable used patient identifier. title (string) title plot. subtitle (string) subtitle plot. caption (string) optional caption plot. add_baseline_hline (flag) adds horizontal line baseline y-value plot TRUE. yvar_baseline (string) variable baseline values . Ignored add_baseline_hline FALSE. ggtheme (theme) optional graphical theme function provided ggplot2 control outlook plot. Use ggplot2::theme() tweak display. col (character) line colors.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create simple line plot over time — h_g_ipp","text":"ggplot line plot.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_g_ipp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create simple line plot over time — h_g_ipp","text":"","code":"library(dplyr) library(nestcolor)  # Select a small sample of data to plot. adlb <- tern_ex_adlb %>%   filter(PARAMCD == \"ALT\", !(AVISIT %in% c(\"SCREENING\", \"BASELINE\"))) %>%   slice(1:36)  p <- h_g_ipp(   df = adlb,   xvar = \"AVISIT\",   yvar = \"AVAL\",   xlab = \"Visit\",   id_var = \"USUBJID\",   ylab = \"SGOT/ALT (U/L)\",   add_baseline_hline = TRUE ) p"},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a KM plot — h_ggkm","title":"Helper function to create a KM plot — h_ggkm","text":"Draw Kaplan-Meier plot using ggplot2.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"h_ggkm(   data,   xticks = NULL,   yval = \"Survival\",   censor_show,   xlab,   ylab,   ylim = NULL,   title,   footnotes = NULL,   max_time = NULL,   lwd = 1,   lty = NULL,   pch = 3,   size = 2,   col = NULL,   ci_ribbon = FALSE,   ggtheme = nestcolor::theme_nest() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a KM plot — h_ggkm","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. yval (string) type plot, plotted y-axis. Options Survival (default) Failure probability. censor_show (flag) whether show censored observations. xlab (string) x-axis label. ylab (string) y-axis label. ylim (numeric(2)) vector containing lower upper limits y-axis, respectively. NULL (default), default scale range used. title (string) plot title. footnotes (string) plot footnotes. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL). lwd (numeric) line width. vector given, length equal number strata survival::survfit(). lty (numeric) line type. vector given, length equal number strata survival::survfit(). pch (string) name symbol character use point symbol indicate censored cases. size (numeric(1)) size censored point symbols. col (character) lines colors. Length vector equal number strata survival::survfit(). ci_ribbon (flag) whether confidence interval drawn around Kaplan-Meier curve. ggtheme (theme) graphical theme provided ggplot2 format Kaplan-Meier plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a KM plot — h_ggkm","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ggkm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a KM plot — h_ggkm","text":"","code":"# \\donttest{ library(dplyr) library(survival)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks,   xlab = \"Days\",   yval = \"Survival\",   ylab = \"Survival Probability\",   title = \"Survival\" ) gg  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for Poisson models — h_glm_count","title":"Helper functions for Poisson models — h_glm_count","text":"Helper functions returns results stats::glm() Poisson Quasi-Poisson distributions needed (see family parameter), MASS::glm.nb() Negative Binomial distributions. Link function GLM log.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for Poisson models — h_glm_count","text":"","code":"h_glm_count(.var, .df_row, variables, distribution, weights)  h_glm_poisson(.var, .df_row, variables, weights)  h_glm_quasipoisson(.var, .df_row, variables, weights)  h_glm_negbin(.var, .df_row, variables, weights)"},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for Poisson models — h_glm_count","text":".var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count() returns results selected model. h_glm_poisson() returns results Poisson model. h_glm_quasipoisson() returns results Quasi-Poisson model. h_glm_negbin() returns results negative binomial model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for Poisson models — h_glm_count","text":"h_glm_count(): Helper function return results selected model (Poisson, Quasi-Poisson, negative binomial). h_glm_poisson(): Helper function return results Poisson model. h_glm_quasipoisson(): Helper function return results Quasi-Poisson model. h_glm_negbin(): Helper function return results negative binomial model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create Cox-PH grobs — h_grob_coxph","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"Grob rtable output h_tbl_coxph_pairwise()","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"h_grob_coxph(   ...,   x = 0,   y = 0,   width = grid::unit(0.4, \"npc\"),   ttheme = gridExtra::ttheme_default(padding = grid::unit(c(1, 0.5), \"lines\"), core =     list(bg_params = list(fill = c(\"grey95\", \"grey90\"), alpha = 0.5))) )"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"... arguments pass h_tbl_coxph_pairwise(). x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"grob table containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_coxph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create Cox-PH grobs — h_grob_coxph","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0) tbl_grob <- h_grob_coxph(   df = data,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARMCD\"),   control_coxph_pw = control_coxph(conf_level = 0.9), x = 0.5, y = 0.5 ) #> Warning: `h_grob_coxph()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid::grid.draw(tbl_grob)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create survival estimation grobs — h_grob_median_surv","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"survival fit transformed grob containing table groups rows characterized N, median 95% confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"h_grob_median_surv(   fit_km,   armval = \"All\",   x = 0.9,   y = 0.9,   width = grid::unit(0.3, \"npc\"),   ttheme = gridExtra::ttheme_default() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\". x (proportion) value 0 1 specifying x-location. y (proportion) value 0 1 specifying y-location. width (grid::unit) width (unit) use printing grob. ttheme (list) see gridExtra::ttheme_default().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"grob table containing statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create survival estimation grobs — h_grob_median_surv","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  grid::grid.newpage() grid.rect(gp = grid::gpar(lty = 1, col = \"pink\", fill = \"gray85\", lwd = 1)) tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_grob_median_surv() %>%   grid::grid.draw() #> Warning: `h_grob_median_surv()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"Two graphical objects obtained, one corresponding row labeling second table numbers patients risk. title = TRUE, third object corresponding table title also obtained.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"h_grob_tbl_at_risk(data, annot_tbl, xlim, title = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"data (data.frame) survival data pre-processed h_data_plot. annot_tbl (data.frame) annotation prepared survival::summary.survfit() includes number patients risk given time points. xlim (numeric(1)) maximum value x-axis (used ensure risk table aligns KM graph). title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"named list two gTree objects title = FALSE: at_risk label, three gTree objects title = TRUE: at_risk, label, title.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_tbl_at_risk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create patient-at-risk grobs — h_grob_tbl_at_risk","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .)  data_plot <- h_data_plot(fit_km = fit_km)  xticks <- h_xticks(data = data_plot)  gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" )  # The annotation table reports the patient at risk for a given strata and # times (`xticks`). annot_tbl <- summary(fit_km, times = xticks) if (is.null(fit_km$strata)) {   annot_tbl <- with(annot_tbl, data.frame(n.risk = n.risk, time = time, strata = \"All\")) } else {   strata_lst <- strsplit(sub(\"=\", \"equals\", levels(annot_tbl$strata)), \"equals\")   levels(annot_tbl$strata) <- matrix(unlist(strata_lst), ncol = 2, byrow = TRUE)[, 2]   annot_tbl <- data.frame(     n.risk = annot_tbl$n.risk,     time = annot_tbl$time,     strata = annot_tbl$strata   ) }  # The annotation table is transformed into a grob. tbl <- h_grob_tbl_at_risk(data = data_plot, annot_tbl = annot_tbl, xlim = max(xticks)) #> Warning: `h_grob_tbl_at_risk()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  # For the representation, the layout is estimated for which the decomposition # of the graphic element is necessary. g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") #> Warning: `h_km_layout()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`.  grid::grid.newpage() pushViewport(viewport(layout = lyt, height = .95, width = .95)) grid.rect(gp = grid::gpar(lty = 1, col = \"purple\", fill = \"gray85\", lwd = 1)) pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 2)) grid.rect(gp = grid::gpar(lty = 1, col = \"orange\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$at_risk) popViewport() pushViewport(viewport(layout.pos.row = 3:4, layout.pos.col = 1)) grid.rect(gp = grid::gpar(lty = 1, col = \"green3\", fill = \"gray85\", lwd = 1)) grid::grid.draw(tbl$label)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"Build y-axis annotation decomposed ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"h_grob_y_annot(ylab, yaxis)"},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"ylab (gtable) y-lab graphical object derived ggplot. yaxis (gtable) y-axis graphical object derived ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"gTree object containing y-axis annotation ggplot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_grob_y_annot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create grid object with y-axis annotation — h_grob_y_annot","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"title\", footnotes = \"footnotes\", yval = \"Survival\" )  g_el <- h_decompose_gg(gg)  grid::grid.newpage() pvp <- grid::plotViewport(margins = c(5, 4, 2, 20)) pushViewport(pvp) grid::grid.draw(h_grob_y_annot(ylab = g_el$ylab, yaxis = g_el$yaxis)) #> Warning: `h_grob_y_annot()` was deprecated in tern 0.9.4. #> ℹ `g_km` now generates `ggplot` objects. This function is no longer used within #>   `tern`. grid.rect(gp = grid::gpar(lty = 1, col = \"gray35\", fill = NA))  # }"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate(person_years, n_events, control = control_incidence_rate())  h_incidence_rate_normal(person_years, n_events, alpha = 0.05)  h_incidence_rate_normal_log(person_years, n_events, alpha = 0.05)  h_incidence_rate_exact(person_years, n_events, alpha = 0.05)  h_incidence_rate_byar(person_years, n_events, alpha = 0.05)"},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for incidence rate — h_incidence_rate","text":"person_years (numeric(1)) total person-years risk. n_events (integer(1)) number events observed. control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level: (proportion) confidence level estimated incidence rate. conf_type: (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit: (string)day, week, month, year (default) indicating time unit data input. num_pt_year: (numeric) time unit desired output (person-years). alpha (numeric(1)) two-sided alpha-level confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for incidence rate — h_incidence_rate","text":"Estimated incidence rate, rate, associated confidence interval, rate_ci.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for incidence rate — h_incidence_rate","text":"h_incidence_rate(): Helper function estimate incidence rate associated confidence interval. h_incidence_rate_normal(): Helper function estimate incidence rate associated confidence interval based normal approximation incidence rate. Unit one person-year. h_incidence_rate_normal_log(): Helper function estimate incidence rate associated confidence interval based normal approximation logarithm incidence rate. Unit one person-year. h_incidence_rate_exact(): Helper function estimate incidence rate associated exact confidence interval. Unit one person-year. h_incidence_rate_byar(): Helper function estimate incidence rate associated Byar's confidence interval. Unit one person-year.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for incidence rate — h_incidence_rate","text":"","code":"h_incidence_rate_normal(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] -0.003859038  0.023859038 #>   h_incidence_rate_normal_log(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.002500977 0.039984382 #>   h_incidence_rate_exact(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001211046 0.036123438 #>   h_incidence_rate_byar(200, 2) #> $rate #> [1] 0.01 #>  #> $rate_ci #> [1] 0.001994207 0.032054171 #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to prepare a KM layout — h_km_layout","title":"Helper function to prepare a KM layout — h_km_layout","text":"Prepares (5 rows) x (2 cols) layout Kaplan-Meier curve.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"h_km_layout(   data,   g_el,   title,   footnotes,   annot_at_risk = TRUE,   annot_at_risk_title = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to prepare a KM layout — h_km_layout","text":"data (data.frame) survival data pre-processed h_data_plot. g_el (list gtable) list obtained h_decompose_gg(). title (string) plot title. footnotes (string) plot footnotes. annot_at_risk (flag) compute add annotation table reporting number patient risk matching main grid Kaplan-Meier curve. annot_at_risk_title (flag) whether \"Patients Risk\" title added annot_at_risk table. effect annot_at_risk FALSE. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to prepare a KM layout — h_km_layout","text":"grid layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper function to prepare a KM layout — h_km_layout","text":"layout corresponds grid two columns five rows unequal dimensions. dimension fixed, curve flexible accommodate remaining free space. left column gets annotation ggplot (y-axis) names strata patient risk tabulation. main constraint width columns must allow writing strata name. right column receive ggplot, legend, x-axis patient risk table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_km_layout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to prepare a KM layout — h_km_layout","text":"","code":"# \\donttest{ library(dplyr) library(survival) library(grid)  fit_km <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) data_plot <- h_data_plot(fit_km = fit_km) xticks <- h_xticks(data = data_plot) gg <- h_ggkm(   data = data_plot,   censor_show = TRUE,   xticks = xticks, xlab = \"Days\", ylab = \"Survival Probability\",   title = \"tt\", footnotes = \"ff\", yval = \"Survival\" ) g_el <- h_decompose_gg(gg) lyt <- h_km_layout(data = data_plot, g_el = g_el, title = \"t\", footnotes = \"f\") grid.show.layout(lyt)  # }"},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for multivariate logistic regression — h_logistic_regression","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Helper functions used calculations logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"h_get_interaction_vars(fit_glm)  h_interaction_coef_name(   interaction_vars,   first_var_with_level,   second_var_with_level )  h_or_cat_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   conf_level = 0.95 )  h_or_cont_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_or_interaction(   odds_ratio_var,   interaction_var,   fit_glm,   at = NULL,   conf_level = 0.95 )  h_simple_term_labels(terms, table)  h_interaction_term_labels(terms1, terms2, table, any = FALSE)  h_glm_simple_term_extract(x, fit_glm)  h_glm_interaction_extract(x, fit_glm)  h_glm_inter_term_extract(odds_ratio_var, interaction_var, fit_glm, ...)  h_logistic_simple_terms(x, fit_glm, conf_level = 0.95)  h_logistic_inter_terms(x, fit_glm, conf_level = 0.95, at = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"fit_glm (glm) logistic regression model fitted stats::glm() \"binomial\" family. Limited functionality also available conditional logistic regression models fitted survival::clogit(), currently used extract_rsp_biomarkers(). interaction_vars (character(2)) interaction variable names. first_var_with_level (character(2)) first variable name interaction level. second_var_with_level (character(2)) second variable name interaction level. odds_ratio_var (string) odds ratio variable. interaction_var (string) interaction variable. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. terms (character) simple terms. table (table) table containing numbers terms. terms1 (character) terms first dimension (rows). terms2 (character) terms second dimension (rows). (flag) whether term1 term2 can fulfilled count number patients. case can scalar (strings). x (character) variable interaction term fit_glm (depending helper function used). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"Vector names interaction variables. Name coefficient. Odds ratio. Odds ratio. Odds ratio. Term labels containing numbers patients. Term labels containing numbers patients. Tabulated main effect results logistic regression model. Tabulated interaction term results logistic regression model. data.frame tabulated interaction term results logistic regression model. Tabulated statistics given variable(s) logistic regression model. Tabulated statistics given variable(s) logistic regression model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"h_get_interaction_vars(): Helper function extract interaction variable names fitted model assuming one interaction term. h_interaction_coef_name(): Helper function get right coefficient name interaction variable names given levels. main value order first second variable checked interaction_vars input. h_or_cat_interaction(): Helper function calculate odds ratio estimates case odds ratio interaction variable categorical. h_or_cont_interaction(): Helper function calculate odds ratio estimates case either odds ratio interaction variable continuous. h_or_interaction(): Helper function calculate odds ratio estimates case interaction. wrapper h_or_cont_interaction() h_or_cat_interaction(). h_simple_term_labels(): Helper function construct term labels simple terms table numbers patients. h_interaction_term_labels(): Helper function construct term labels interaction terms table numbers patients. h_glm_simple_term_extract(): Helper function tabulate main effect results (conditional) logistic regression model. h_glm_interaction_extract(): Helper function tabulate interaction term results logistic regression model. h_glm_inter_term_extract(): Helper function tabulate interaction results logistic regression model. basically wrapper h_or_interaction() h_glm_simple_term_extract() puts results right data frame format. h_logistic_simple_terms(): Helper function tabulate results including odds ratios confidence intervals simple terms. h_logistic_inter_terms(): Helper function tabulate results including odds ratios confidence intervals interaction terms.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"provide function case variables continuous arise table, treatment arm variable always involved categorical.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_logistic_regression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for multivariate logistic regression — h_logistic_regression","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  h_glm_simple_term_extract(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary #> 1               FALSE            TRUE h_glm_simple_term_extract(\"ARMCD\", mod1) #>   variable   variable_label  term              term_label interaction #> 1    ARMCD Planned Arm Code ARM A Reference ARM A, n = 64             #> 2    ARMCD Planned Arm Code ARM B           ARM B, n = 68             #> 3    ARMCD Planned Arm Code ARM C           ARM C, n = 52             #>   interaction_label reference reference_label  estimate std_error df    pvalue #> 1                                                                  2 0.3004308 #> 2                                             -1.774769  1.144405  1 0.1209443 #> 3                                               17.1922  3626.588  1 0.9962176 #>   is_variable_summary is_term_summary #> 1                TRUE           FALSE #> 2               FALSE            TRUE #> 3               FALSE            TRUE  h_glm_interaction_extract(\"ARMCD:AGE\", mod2) #>    variable                        variable_label  term              term_label #> 1 ARMCD:AGE Interaction of Planned Arm Code * Age ARM A Reference ARM A, n = 64 #> 2 ARMCD:AGE Interaction of Planned Arm Code * Age ARM B           ARM B, n = 68 #> 3 ARMCD:AGE Interaction of Planned Arm Code * Age ARM C           ARM C, n = 52 #>   interaction interaction_label reference reference_label   estimate std_error #> 1                                                                              #> 2                                                          0.3081205 0.2062392 #> 3                                                         0.02948826  548.5923 #>   df    pvalue is_variable_summary is_term_summary #> 1  2 0.3275837                TRUE           FALSE #> 2  1 0.1351767               FALSE            TRUE #> 3  1 0.9999571               FALSE            TRUE  h_glm_inter_term_extract(\"AGE\", \"ARMCD\", mod2) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #> 2      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 3      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #> 4      AGE            Age  AGE        Age       ARMCD  Planned Arm Code #>   reference reference_label    estimate std_error odds_ratio       lcl      ucl #> 1                           -0.03873898 0.1514322         NA        NA       NA #> 2     ARM A           ARM A          NA        NA  0.9620018 0.7149514 1.294420 #> 3     ARM B           ARM B          NA        NA  1.3091545 1.0021802 1.710157 #> 4     ARM C           ARM C          NA        NA  0.9907919 0.0000000      Inf #>   df   pvalue is_variable_summary is_term_summary is_reference_summary #> 1  1 0.798092               FALSE            TRUE                FALSE #> 2 NA       NA               FALSE           FALSE                 TRUE #> 3 NA       NA               FALSE           FALSE                 TRUE #> 4 NA       NA               FALSE           FALSE                 TRUE  h_logistic_simple_terms(\"AGE\", mod1) #>   variable variable_label term term_label interaction interaction_label #> 1      AGE            Age  AGE        Age                               #>   reference reference_label  estimate  std_error df     pvalue #> 1                           0.1698216 0.09524116  1 0.07457501 #>   is_variable_summary is_term_summary odds_ratio       lcl      ucl #> 1               FALSE            TRUE   1.185093 0.9832935 1.428308 #>                     ci #> 1 0.9832935, 1.4283084  h_logistic_inter_terms(c(\"RACE\", \"AGE\", \"ARMCD\", \"AGE:ARMCD\"), mod2) #>        variable                        variable_label                      term #> 1          RACE                                  Race                     ASIAN #> 2          RACE                                  Race BLACK OR AFRICAN AMERICAN #> 3          RACE                                  Race                     WHITE #> 13        ARMCD                      Planned Arm Code                     ARM A #> 23        ARMCD                      Planned Arm Code                     ARM B #> ARM B     ARMCD                      Planned Arm Code                     ARM B #> 33        ARMCD                      Planned Arm Code                     ARM C #> ARM C     ARMCD                      Planned Arm Code                     ARM C #> 11          AGE                                   Age                       AGE #> 21          AGE                                   Age                       AGE #> 31          AGE                                   Age                       AGE #> 4           AGE                                   Age                       AGE #> 12    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM A #> 22    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM B #> 32    AGE:ARMCD Interaction of Planned Arm Code * Age                     ARM C #>                              term_label interaction interaction_label reference #> 1              Reference ASIAN, n = 110                                         #> 2     BLACK OR AFRICAN AMERICAN, n = 40                                         #> 3                         WHITE, n = 34                                         #> 13              Reference ARM A, n = 64                                         #> 23                        ARM B, n = 68                                         #> ARM B                     ARM B, n = 68         AGE               Age        35 #> 33                        ARM C, n = 52                                         #> ARM C                     ARM C, n = 52         AGE               Age        35 #> 11                                  Age                                         #> 21                                  Age       ARMCD  Planned Arm Code     ARM A #> 31                                  Age       ARMCD  Planned Arm Code     ARM B #> 4                                   Age       ARMCD  Planned Arm Code     ARM C #> 12              Reference ARM A, n = 64                                         #> 22                        ARM B, n = 68                                         #> 32                        ARM C, n = 52                                         #>       reference_label    estimate std_error df     pvalue odds_ratio        lcl #> 1                                            2  0.9361139                       #> 2                        18.15018  3944.701  1  0.9963288   76299564          0 #> 3                      -0.3727152  1.025808  1  0.7163522  0.6888614 0.09224926 #> 13                                           2   0.253914         NA         NA #> 23                      -11.52715   6.96188  1 0.09777185         NA         NA #> ARM B              35          NA        NA NA         NA  0.4757148 0.03361147 #> 33                       16.33327  20278.39  1  0.9993573         NA         NA #> ARM C              35          NA        NA NA         NA   34808099          0 #> 11                    -0.03873898 0.1514322  1   0.798092         NA         NA #> 21              ARM A          NA        NA NA         NA  0.9620018  0.7149514 #> 31              ARM B          NA        NA NA         NA   1.309155    1.00218 #> 4               ARM C          NA        NA NA         NA  0.9907919          0 #> 12                                          NA         NA         NA         NA #> 22                      0.3081205 0.2062392  1  0.1351767         NA         NA #> 32                     0.02948826  548.5923  1  0.9999571         NA         NA #>            ucl is_variable_summary is_term_summary is_reference_summary #> 1                             TRUE           FALSE                FALSE #> 2          Inf               FALSE            TRUE                FALSE #> 3     5.143998               FALSE            TRUE                FALSE #> 13          NA                TRUE           FALSE                FALSE #> 23          NA               FALSE            TRUE                FALSE #> ARM B 6.732956               FALSE           FALSE                 TRUE #> 33          NA               FALSE            TRUE                FALSE #> ARM C      Inf               FALSE           FALSE                 TRUE #> 11          NA               FALSE            TRUE                FALSE #> 21     1.29442               FALSE           FALSE                 TRUE #> 31    1.710157               FALSE           FALSE                 TRUE #> 4          Inf               FALSE           FALSE                 TRUE #> 12          NA                TRUE           FALSE                FALSE #> 22          NA               FALSE            TRUE                FALSE #> 32          NA               FALSE            TRUE                FALSE #>                           ci #> 1                            #> 2                     0, Inf #> 3     0.09224926, 5.14399810 #> 13                    NA, NA #> 23                    NA, NA #> ARM B 0.03361147, 6.73295611 #> 33                    NA, NA #> ARM C                 0, Inf #> 11                    NA, NA #> 21      0.7149514, 1.2944200 #> 31        1.002180, 1.710157 #> 4                     0, Inf #> 12                    NA, NA #> 22                    NA, NA #> 32                    NA, NA"},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"Helper function create map data frame input dataset, can used argument trim_levels_to_map split function. Based different method, map constructed differently.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"h_map_for_count_abnormal(   df,   variables = list(anl = \"ANRIND\", split_rows = c(\"PARAM\"), range_low = \"ANRLO\",     range_high = \"ANRHI\"),   abnormal = list(low = c(\"LOW\", \"LOW LOW\"), high = c(\"HIGH\", \"HIGH HIGH\")),   method = c(\"default\", \"range\"),   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"df (data.frame) data set containing analysis variables. variables (named list string) list additional analysis variables. abnormal (named list) identifying abnormal range level(s) df. Based levels abnormality input dataset, can something like list(Low = \"LOW LOW\", High = \"HIGH HIGH\") abnormal = list(Low = \"LOW\", High = \"HIGH\")) method (string) indicates returned map constructed. Can \"default\" \"range\". na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"map data.frame.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"method \"default\", returned map abnormal directions observed df, records normal values excluded avoid error creating layout. method \"range\", returned map based rule least one observation low range > 0 low direction least one observation high range missing high direction.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_map_for_count_abnormal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a map data frame for trim_levels_to_map() — h_map_for_count_abnormal","text":"","code":"adlb <- df_explicit_na(tern_ex_adlb)  h_map_for_count_abnormal(   df = adlb,   variables = list(anl = \"ANRIND\", split_rows = c(\"LBCAT\", \"PARAM\")),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"default\",   na_str = \"<Missing>\" ) #>        LBCAT                                PARAM ANRIND #> 1  CHEMISTRY Alanine Aminotransferase Measurement    LOW #> 4  CHEMISTRY Alanine Aminotransferase Measurement   HIGH #> 7  CHEMISTRY Alanine Aminotransferase Measurement NORMAL #> 2  CHEMISTRY       C-Reactive Protein Measurement    LOW #> 3  CHEMISTRY       C-Reactive Protein Measurement   HIGH #> 8  CHEMISTRY       C-Reactive Protein Measurement NORMAL #> 5 IMMUNOLOGY         Immunoglobulin A Measurement    LOW #> 6 IMMUNOLOGY         Immunoglobulin A Measurement   HIGH #> 9 IMMUNOLOGY         Immunoglobulin A Measurement NORMAL  df <- data.frame(   USUBJID = c(rep(\"1\", 4), rep(\"2\", 4), rep(\"3\", 4)),   AVISIT = c(     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2),     rep(\"WEEK 1\", 2),     rep(\"WEEK 2\", 2)   ),   PARAM = rep(c(\"ALT\", \"CPR\"), 6),   ANRIND = c(     \"NORMAL\", \"NORMAL\", \"LOW\",     \"HIGH\", \"LOW\", \"LOW\", \"HIGH\", \"HIGH\", rep(\"NORMAL\", 4)   ),   ANRLO = rep(5, 12),   ANRHI = rep(20, 12) ) df$ANRIND <- factor(df$ANRIND, levels = c(\"LOW\", \"HIGH\", \"NORMAL\")) h_map_for_count_abnormal(   df = df,   variables = list(     anl = \"ANRIND\",     split_rows = c(\"PARAM\"),     range_low = \"ANRLO\",     range_high = \"ANRHI\"   ),   abnormal = list(low = c(\"LOW\"), high = c(\"HIGH\")),   method = \"range\",   na_str = \"<Missing>\" ) #>   PARAM ANRIND #> 1   ALT    LOW #> 3   ALT   HIGH #> 5   ALT NORMAL #> 2   CPR    LOW #> 4   CPR   HIGH #> 6   CPR NORMAL"},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for odds ratio estimation — h_odds_ratio","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"Functions calculate odds ratios estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"or_glm(data, conf_level)  or_clogit(data, conf_level, method = \"exact\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"data (data.frame) data frame containing least variables rsp grp, optionally strata or_clogit(). conf_level (proportion) confidence level interval. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"named list elements or_ci n_tot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"or_glm(): Estimates odds ratio based stats::glm(). Note must exactly 2 groups data specified grp variable. or_clogit(): Estimates odds ratio based survival::clogit(). done whole data set including groups, since results pairwise comparisons groups.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for odds ratio estimation — h_odds_ratio","text":"","code":"# Data with 2 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1)),   grp = letters[c(1, 1, 1, 2, 2, 2, 1, 2)],   strata = letters[c(1, 2, 1, 2, 2, 2, 1, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on glm. or_glm(data, conf_level = 0.95) #> $or_ci #>        est        lcl        ucl  #> 0.33333333 0.01669735 6.65441589  #>  #> $n_tot #> n_tot  #>     8  #>   # Data with 3 groups. data <- data.frame(   rsp = as.logical(c(1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0)),   grp = letters[c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3)],   strata = LETTERS[c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2)],   stringsAsFactors = TRUE )  # Odds ratio based on stratified estimation by conditional logistic regression. or_clogit(data, conf_level = 0.95) #> $or_ci #> $or_ci$b #>        est        lcl        ucl  #> 0.28814553 0.02981009 2.78522598  #>  #> $or_ci$c #>       est       lcl       ucl  #> 0.5367919 0.0673365 4.2791881  #>  #>  #> $n_tot #> n_tot  #>    20  #>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"h_pkparam_sort(pk_data, key_var = \"PARAMCD\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pk_data (data.frame) pharmacokinetic data frame. key_var (string) key variable used merge pk_data metadata created d_pkparam().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"pharmacokinetic data.frame sorted PARAM variable.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_pkparam_sort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort pharmacokinetic data by PARAM variable — h_pkparam_sort","text":"","code":"library(dplyr)  adpp <- tern_ex_adpp %>% mutate(PKPARAM = factor(paste0(PARAM, \" (\", AVALU, \")\"))) pk_ordered_data <- h_pkparam_sort(adpp)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to return the estimated means using predicted probabilities — h_ppmeans","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"arm level, predicted mean rate calculated using fitted model object, newdata set result stats::model.frame, reconstructed data original data, depending object formula (coming fit). confidence interval derived using conf_level parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"","code":"h_ppmeans(obj, .df_row, arm, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"obj (glm.fit) fitted model object used derive mean rate estimates treatment arm. .df_row (data.frame) dataset includes variables called .var variables. arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. conf_level (proportion) value used derive confidence interval rate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_ppmeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to return the estimated means using predicted probabilities — h_ppmeans","text":"h_ppmeans() returns estimated means.","code":""},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"prop_diff_wald(rsp, grp, conf_level = 0.95, correct = FALSE)  prop_diff_ha(rsp, grp, conf_level)  prop_diff_nc(rsp, grp, conf_level, correct = FALSE)  prop_diff_cmh(rsp, grp, strata, conf_level = 0.95)  prop_diff_strat_nc(   rsp,   grp,   strata,   weights_method = c(\"cmh\", \"wilson_h\"),   conf_level = 0.95,   correct = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"rsp (logical) vector indicating whether subject responder . grp (factor) vector assigning observations one two groups (e.g. reference treatment group). conf_level (proportion) confidence level interval. correct (flag) whether include continuity correction. information, see stats::prop.test(). strata (factor) variable one level per stratum length rsp. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"named list elements diff (proportion difference) diff_ci (proportion difference confidence interval).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"prop_diff_wald(): Wald interval follows usual textbook definition single proportion confidence interval using normal approximation. possible include continuity correction Wald's interval. prop_diff_ha(): Anderson-Hauck confidence interval. prop_diff_nc(): Newcombe confidence interval. based Wilson score confidence interval single binomial proportion. prop_diff_cmh(): Calculates weighted difference. defined difference response rates experimental treatment group control treatment group, adjusted stratification factors applying Cochran-Mantel-Haenszel (CMH) weights. CMH chi-squared test, use stats::mantelhaen.test(). prop_diff_strat_nc(): Calculates stratified Newcombe confidence interval difference response rates experimental treatment group control treatment group, adjusted stratification factors. implementation follows closely one proposed Yan2010-jt;textualtern. Weights can estimated heuristic proposed prop_strat_wilson() CMH-derived weights (see prop_diff_cmh()).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions to calculate proportion difference — h_prop_diff","text":"","code":"# Wald confidence interval set.seed(2) rsp <- sample(c(TRUE, FALSE), replace = TRUE, size = 20) grp <- factor(c(rep(\"A\", 10), rep(\"B\", 10)))  prop_diff_wald(rsp = rsp, grp = grp, conf_level = 0.95, correct = FALSE) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.4382613  0.4382613 #>   # Anderson-Hauck confidence interval ## \"Mid\" case: 3/4 respond in group A, 1/2 respond in group B. rsp <- c(TRUE, FALSE, FALSE, TRUE, TRUE, TRUE) grp <- factor(c(\"A\", \"B\", \"A\", \"B\", \"A\", \"A\"), levels = c(\"B\", \"A\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.90) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] -0.9195011  1.0000000 #>   ## Edge case: Same proportion of response in A and B. rsp <- c(TRUE, FALSE, TRUE, FALSE) grp <- factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\"))  prop_diff_ha(rsp = rsp, grp = grp, conf_level = 0.6) #> $diff #> [1] 0 #>  #> $diff_ci #> [1] -0.8451161  0.8451161 #>   # Newcombe confidence interval  set.seed(1) rsp <- c(   sample(c(TRUE, FALSE), size = 40, prob = c(3 / 4, 1 / 4), replace = TRUE),   sample(c(TRUE, FALSE), size = 40, prob = c(1 / 2, 1 / 2), replace = TRUE) ) grp <- factor(rep(c(\"A\", \"B\"), each = 40), levels = c(\"B\", \"A\")) table(rsp, grp) #>        grp #> rsp      B  A #>   FALSE 20 10 #>   TRUE  20 30  prop_diff_nc(rsp = rsp, grp = grp, conf_level = 0.9) #> $diff #> [1] 0.25 #>  #> $diff_ci #> [1] 0.07193388 0.40725819 #>   # Cochran-Mantel-Haenszel confidence interval  set.seed(2) rsp <- sample(c(TRUE, FALSE), 100, TRUE) grp <- sample(c(\"Placebo\", \"Treatment\"), 100, TRUE) grp <- factor(grp, levels = c(\"Placebo\", \"Treatment\")) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_cmh(   rsp = rsp, grp = grp, strata = interaction(strata_data),   conf_level = 0.90 ) #> $prop #>   Placebo Treatment  #> 0.5331117 0.3954251  #>  #> $prop_ci #> $prop_ci$Placebo #> [1] 0.4306536 0.6355698 #>  #> $prop_ci$Treatment #> [1] 0.2890735 0.5017768 #>  #>  #> $diff #> [1] -0.1376866 #>  #> $diff_ci #> [1] -0.285363076  0.009989872 #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.1148388 0.2131696 0.1148388 0.2131696 0.1767914 0.1671918  #>  #> $n1 #> a.x b.x a.y b.y a.z b.z  #>   4  11   8  11  13  11  #>  #> $n2 #> a.x b.x a.y b.y a.z b.z  #>   8   9   4   9   6   6  #>   # Stratified Newcombe confidence interval  set.seed(2) data_set <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   \"grp\" = sample(c(\"Placebo\", \"Treatment\"), 100, TRUE),   stringsAsFactors = TRUE )  prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"cmh\",   conf_level = 0.90 ) #> $diff #> [1] -0.05777672 #>  #> $diff_ci #>      lower      upper  #> -0.2236537  0.1119331  #>   prop_diff_strat_nc(   rsp = data_set$rsp, grp = data_set$grp, strata = interaction(data_set[2:3]),   weights_method = \"wilson_h\",   conf_level = 0.90 ) #> $diff #> [1] -0.07771884 #>  #> $diff_ci #>      lower      upper  #> -0.2540844  0.1027720  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions to test proportion differences — h_prop_diff_test","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"Helper functions implement various tests difference two proportions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"","code":"prop_chisq(tbl)  prop_cmh(ary)  prop_schouten(tbl)  prop_fisher(tbl)"},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"tbl (matrix) matrix two groups rows binary response (TRUE/FALSE) columns. ary (array, 3 dimensions) array two groups rows, binary response (TRUE/FALSE) columns, strata third dimension.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions to test proportion differences — h_prop_diff_test","text":"prop_chisq(): Performs Chi-Squared test. Internally calls stats::prop.test(). prop_cmh(): Performs stratified Cochran-Mantel-Haenszel test. Internally calls stats::mantelhaen.test(). Note strata less two observations automatically discarded. prop_schouten(): Performs Chi-Squared test Schouten correction. prop_fisher(): Performs Fisher's exact test. Internally calls stats::fisher.test().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for calculating proportion confidence intervals — h_proportions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Functions calculate different proportion confidence intervals use estimate_proportion().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"prop_wilson(rsp, conf_level, correct = FALSE)  prop_strat_wilson(   rsp,   strata,   weights = NULL,   conf_level = 0.95,   max_iterations = NULL,   correct = FALSE )  prop_clopper_pearson(rsp, conf_level)  prop_wald(rsp, conf_level, correct = FALSE)  prop_agresti_coull(rsp, conf_level)  prop_jeffreys(rsp, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"rsp (logical) vector indicating whether subject responder . conf_level (proportion) confidence level interval. correct (flag) whether apply continuity correction. strata (factor) variable one level per stratum length rsp. weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. max_iterations (count) maximum number iterations iterative procedure used find estimates optimal weights.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Confidence interval proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"prop_wilson(): Calculates Wilson interval calling stats::prop.test(). Also referred Wilson score interval. prop_strat_wilson(): Calculates stratified Wilson confidence interval unequal proportions described Yan2010-jt;textualtern prop_clopper_pearson(): Calculates Clopper-Pearson interval calling stats::binom.test(). Also referred exact method. prop_wald(): Calculates Wald interval following usual textbook definition single proportion confidence interval using normal approximation. prop_agresti_coull(): Calculates Agresti-Coull interval. Constructed (95% CI) adding two successes two failures data using Wald formula construct CI. prop_jeffreys(): Calculates Jeffreys interval, equal-tailed interval based non-informative Jeffreys prior binomial proportion.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"Yan2010-jttern","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_proportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for calculating proportion confidence intervals — h_proportions","text":"","code":"rsp <- c(   TRUE, TRUE, TRUE, TRUE, TRUE,   FALSE, FALSE, FALSE, FALSE, FALSE ) prop_wilson(rsp, conf_level = 0.9) #> [1] 0.2692718 0.7307282  # Stratified Wilson confidence interval with unequal probabilities  set.seed(1) rsp <- sample(c(TRUE, FALSE), 100, TRUE) strata_data <- data.frame(   \"f1\" = sample(c(\"a\", \"b\"), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE ) strata <- interaction(strata_data) n_strata <- ncol(table(rsp, strata)) # Number of strata  prop_strat_wilson(   rsp = rsp, strata = strata,   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4072891 0.5647887  #>  #> $weights #>       a.x       b.x       a.y       b.y       a.z       b.z  #> 0.2074199 0.1776464 0.1915610 0.1604678 0.1351096 0.1277952  #>   # Not automatic setting of weights prop_strat_wilson(   rsp = rsp, strata = strata,   weights = rep(1 / n_strata, n_strata),   conf_level = 0.90 ) #> $conf_int #>     lower     upper  #> 0.4190436 0.5789733  #>   prop_clopper_pearson(rsp, conf_level = .95) #> [1] 0.3886442 0.5919637  prop_wald(rsp, conf_level = 0.95) #> [1] 0.3920214 0.5879786 prop_wald(rsp, conf_level = 0.95, correct = TRUE) #> [1] 0.3870214 0.5929786  prop_agresti_coull(rsp, conf_level = 0.95) #> [1] 0.3942193 0.5865206  prop_jeffreys(rsp, conf_level = 0.95) #> [1] 0.3934779 0.5870917"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"h_rsp_to_logistic_variables(variables, biomarker)  h_logistic_mult_cont_df(variables, data, control = control_logistic())  h_tab_rsp_one_biomarker(df, vars, na_str = default_na_str(), .indent_mods = 0L)"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (named list) controls response definition confidence level produced control_logistic(). df (data.frame) results single biomarker, part returned extract_rsp_biomarkers() (needs couple columns added high-level function relative returned h_logistic_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables() returns named list elements response, arm, covariates, strata. h_logistic_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_rsp_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"h_rsp_to_logistic_variables(): helps converting \"response\" function variable list \"logistic regression\" variable list. reason currently inconsistency variable names accepted extract_rsp_subgroups() fit_logistic(). h_logistic_mult_cont_df(): prepares estimates number responses, patients overall response rate, well odds ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements rsp biomarkers (vector continuous biomarker variables) optionally covariates strata. h_tab_rsp_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on binary response by subgroup — h_response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # This is how the variable list is converted internally. h_rsp_to_logistic_variables(   variables = list(     rsp = \"RSP\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $response #> [1] \"RSP\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_logistic_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\"   ),   data = adrs_f ) df #>   biomarker              biomarker_label n_tot n_rsp prop        or       lcl #> 1    BMRKR1 Continuous Level Biomarker 1   200   164 0.82 0.9755036 0.8804862 #> 2       AGE                          Age   200   164 0.82 0.9952416 0.9462617 #>        ucl conf_level      pval     pval_label #> 1 1.080775       0.95 0.6352602 p-value (Wald) #> 2 1.046757       0.95 0.8530389 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = \"STRATA1\"   ),   data = adrs_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\"  h_tab_rsp_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\") ) #>                Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200        164          82.0%          0.98      (0.88, 1.08)       0.6353"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Helper functions tabulate data frame statistics response rate odds ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"h_proportion_df(rsp, arm)  h_proportion_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_odds_ratio_df(rsp, arm, strata_data = NULL, conf_level = 0.95, method = NULL)  h_odds_ratio_subgroups_df(   variables,   data,   groups_lists = list(),   conf_level = 0.95,   method = NULL,   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"rsp (logical) vector indicating whether subject responder . arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. conf_level (proportion) confidence level interval. method (string NULL) specifies test used calculate p-value difference two proportions. options, see test_proportion_diff(). Default NULL test performed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df() returns data.frame columns arm, n, n_rsp, prop. h_proportion_subgroups_df() returns data.frame columns arm, n, n_rsp, prop, subgroup, var, var_label, row_type. h_odds_ratio_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, optionally pval pval_label. h_odds_ratio_subgroups_df() returns data.frame columns arm, n_tot, , lcl, ucl, conf_level, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"h_proportion_df(): Helper prepare data frame binary responses arm. h_proportion_subgroups_df(): Summarizes proportion binary responses arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_odds_ratio_df(): Helper prepare data frame estimates odds ratio treatment control arm. h_odds_ratio_subgroups_df(): Summarizes estimates odds ratio treatment control arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements rsp, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating binary response by subgroup — h_response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  h_proportion_df(   c(TRUE, FALSE, FALSE),   arm = factor(c(\"A\", \"A\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n n_rsp prop #> 1   A 2     1  0.5 #> 2   B 1     0  0.0  h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_proportion_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Unstratatified analysis. h_odds_ratio_df(   c(TRUE, FALSE, FALSE, TRUE),   arm = factor(c(\"A\", \"A\", \"B\", \"B\"), levels = c(\"A\", \"B\")) ) #>   arm n_tot or        lcl      ucl conf_level #> 1         4  1 0.01984252 50.39681       0.95  # Include p-value. h_odds_ratio_df(adrs_f$rsp, adrs_f$ARM, method = \"chisq\") #>   arm n_tot    or      lcl      ucl conf_level       pval #> 1       142 2.714 1.180449 6.239827       0.95 0.01643036 #>                   pval_label #> 1 p-value (Chi-Squared Test)  # Stratatified analysis. h_odds_ratio_df(   rsp = adrs_f$rsp,   arm = adrs_f$ARM,   strata_data = adrs_f[, c(\"STRATA1\", \"STRATA2\")],   method = \"cmh\" ) #>   arm n_tot       or      lcl      ucl conf_level       pval #> 1       142 2.665586 1.146149 6.199324       0.95 0.02019665 #>                               pval_label #> 1 p-value (Cochran-Mantel-Haenszel Test)  # Unstratified analysis. h_odds_ratio_subgroups_df(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Stratified analysis. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adrs_f ) #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6655860 1.1461490  6.199324       0.95 All Patients    ALL #> 2        78 7.7065093 1.5817529 37.547132       0.95            F    SEX #> 3        64 0.9572284 0.2990954  3.063525       0.95            M    SEX #> 4        50 3.0323726 0.8833232 10.409875       0.95          LOW BMRKR2 #> 5        49 2.1264996 0.4312008 10.486995       0.95       MEDIUM BMRKR2 #> 6        43 2.5134820 0.4351747 14.517370       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_odds_ratio_subgroups_df(   variables = list(     rsp = \"rsp\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split data frame by subgroups — h_split_by_subgroups","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Split data frame non-nested list subsets.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"h_split_by_subgroups(data, subgroups, groups_lists = list())"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split data frame by subgroups — h_split_by_subgroups","text":"data (data.frame) dataset split. subgroups (character) names factor variables data used create subsets. Unused levels present data dropped. Note order vector determines order downstream table. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split data frame by subgroups — h_split_by_subgroups","text":"list subset data (df) metadata subset (df_labels).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split data frame by subgroups — h_split_by_subgroups","text":"Main functionality prepare data use forest plot layouts.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_by_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split data frame by subgroups — h_split_by_subgroups","text":"","code":"df <- data.frame(   x = c(1:5),   y = factor(c(\"A\", \"B\", \"A\", \"B\", \"A\"), levels = c(\"A\", \"B\", \"C\")),   z = factor(c(\"C\", \"C\", \"D\", \"D\", \"D\"), levels = c(\"D\", \"C\")) ) formatters::var_labels(df) <- paste(\"label for\", names(df))  h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\") ) #> $y.A #> $y.A$df #>   x y z #> 1 1 A C #> 2 3 A D #> 3 5 A D #>  #> $y.A$df_labels #>   subgroup var   var_label #> 1        A   y label for y #>  #>  #> $y.B #> $y.B$df #>   x y z #> 1 2 B C #> 2 4 B D #>  #> $y.B$df_labels #>   subgroup var   var_label #> 1        B   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>   h_split_by_subgroups(   data = df,   subgroups = c(\"y\", \"z\"),   groups_lists = list(     y = list(\"AB\" = c(\"A\", \"B\"), \"C\" = \"C\")   ) ) #> $y.AB #> $y.AB$df #>   x y z #> 1 1 A C #> 2 2 B C #> 3 3 A D #> 4 4 B D #> 5 5 A D #>  #> $y.AB$df_labels #>   subgroup var   var_label #> 1       AB   y label for y #>  #>  #> $z.D #> $z.D$df #>   x y z #> 1 3 A D #> 2 4 B D #> 3 5 A D #>  #> $z.D$df_labels #>   subgroup var   var_label #> 1        D   z label for z #>  #>  #> $z.C #> $z.C$df #>   x y z #> 1 1 A C #> 2 2 B C #>  #> $z.C$df_labels #>   subgroup var   var_label #> 1        C   z label for z #>  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":null,"dir":"Reference","previous_headings":"","what":"Split parameters — h_split_param","title":"Split parameters — h_split_param","text":"divides data vector param groups defined f based specified values. relevant rtables layers distribute parameters .stats ' .formats lists items corresponding specific analysis function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split parameters — h_split_param","text":"","code":"h_split_param(param, value, f)"},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split parameters — h_split_param","text":"param (vector) parameter split. value (vector) value used split. f (list) reference make split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split parameters — h_split_param","text":"named list element names f, containing elements specified .stats.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_split_param.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split parameters — h_split_param","text":"","code":"f <- list(   surv = c(\"pt_at_risk\", \"event_free_rate\", \"rate_se\", \"rate_ci\"),   surv_diff = c(\"rate_diff\", \"rate_diff_ci\", \"ztest_pval\") )  .stats <- c(\"pt_at_risk\", \"rate_diff\") h_split_param(.stats, .stats, f = f) #> $surv #> [1] \"pt_at_risk\" #>  #> $surv_diff #> [1] \"rate_diff\" #>   # $surv # [1] \"pt_at_risk\" # # $surv_diff # [1] \"rate_diff\"  .formats <- c(\"pt_at_risk\" = \"xx\", \"event_free_rate\" = \"xxx\") h_split_param(.formats, names(.formats), f = f) #> $surv #>      pt_at_risk event_free_rate  #>            \"xx\"           \"xxx\"  #>  #> $surv_diff #> NULL #>   # $surv # pt_at_risk event_free_rate # \"xx\"           \"xxx\" # # $surv_diff # NULL"},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"Helper function create new SMQ variable ADAE consists adverse events belonging selected Standardized/Customized queries. new dataset contain records adverse events belonging selected baskets. Remember na_str must match needed pre-processing done df_explicit_na() desired output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"h_stack_by_baskets(   df,   baskets = grep(\"^(SMQ|CQ).+NAM$\", names(df), value = TRUE),   smq_varlabel = \"Standardized MedDRA Query\",   keys = c(\"STUDYID\", \"USUBJID\", \"ASTDTM\", \"AEDECOD\", \"AESEQ\"),   aag_summary = NULL,   na_str = \"<Missing>\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"df (data.frame) data set containing analysis variables. baskets (character) variable names selected Standardized/Customized queries. smq_varlabel (string) label new variable created. keys (character) names key variables returned along new variable created. aag_summary (data.frame) containing SMQ baskets levels interest final SMQ variable. useful levels interest observed df dataset. two columns dataset named basket basket_name. na_str (string) string used replace NA empty values output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"data.frame variables keys taken df new variable SMQ containing records belonging baskets selected via baskets argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_stack_by_baskets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to create a new SMQ variable in ADAE by stacking SMQ and/or CQ records. — h_stack_by_baskets","text":"","code":"adae <- tern_ex_adae[1:20, ] %>% df_explicit_na() h_stack_by_baskets(df = adae) #> # A tibble: 8 × 6 #>   STUDYID USUBJID               ASTDTM              AEDECOD       AESEQ SMQ      #>   <fct>   <fct>                 <dttm>              <fct>         <int> <fct>    #> 1 AB12345 AB12345-BRA-11-id-8   2021-12-05 02:02:07 dcd D.2.1.5.3     2 D.2.1.5… #> 2 AB12345 AB12345-BRA-12-id-120 2020-02-05 01:42:29 dcd D.2.1.5.3     2 D.2.1.5… #> 3 AB12345 AB12345-BRA-1-id-171  2022-11-29 12:18:31 dcd C.1.1.1.3     2 C.1.1.1… #> 4 AB12345 AB12345-BRA-1-id-23   2020-07-10 07:32:49 dcd B.2.2.3.1     3 C.1.1.1… #> 5 AB12345 AB12345-BRA-1-id-59   2021-10-10 23:54:46 dcd C.1.1.1.3     4 C.1.1.1… #> 6 AB12345 AB12345-BRA-1-id-9    2021-06-01 14:39:09 dcd C.1.1.1.3     1 C.1.1.1… #> 7 AB12345 AB12345-BRA-11-id-8   2021-12-21 02:02:07 dcd C.1.1.1.3     3 C.1.1.1… #> 8 AB12345 AB12345-BRA-12-id-120 2020-10-01 01:42:29 dcd C.1.1.1.3     3 C.1.1.1…  aag <- data.frame(   NAMVAR = c(\"CQ01NAM\", \"CQ02NAM\", \"SMQ01NAM\", \"SMQ02NAM\"),   REFNAME = c(     \"D.2.1.5.3/A.1.1.1.1 aesi\", \"X.9.9.9.9/Y.8.8.8.8 aesi\",     \"C.1.1.1.3/B.2.2.3.1 aesi\", \"C.1.1.1.3/B.3.3.3.3 aesi\"   ),   SCOPE = c(\"\", \"\", \"BROAD\", \"BROAD\"),   stringsAsFactors = FALSE )  basket_name <- character(nrow(aag)) cq_pos <- grep(\"^(CQ).+NAM$\", aag$NAMVAR) smq_pos <- grep(\"^(SMQ).+NAM$\", aag$NAMVAR) basket_name[cq_pos] <- aag$REFNAME[cq_pos] basket_name[smq_pos] <- paste0(   aag$REFNAME[smq_pos], \"(\", aag$SCOPE[smq_pos], \")\" )  aag_summary <- data.frame(   basket = aag$NAMVAR,   basket_name = basket_name,   stringsAsFactors = TRUE )  result <- h_stack_by_baskets(df = adae, aag_summary = aag_summary) all(levels(aag_summary$basket_name) %in% levels(result$SMQ)) #> [1] TRUE  h_stack_by_baskets(   df = adae,   aag_summary = NULL,   keys = c(\"STUDYID\", \"USUBJID\", \"AEDECOD\", \"ARM\"),   baskets = \"SMQ01NAM\" ) #> # A tibble: 6 × 5 #>   STUDYID USUBJID               AEDECOD       ARM            SMQ                 #>   <fct>   <fct>                 <fct>         <fct>          <fct>               #> 1 AB12345 AB12345-BRA-1-id-171  dcd C.1.1.1.3 B: Placebo     C.1.1.1.3/B.2.2.3.… #> 2 AB12345 AB12345-BRA-1-id-23   dcd B.2.2.3.1 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 3 AB12345 AB12345-BRA-1-id-59   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 4 AB12345 AB12345-BRA-1-id-9    dcd C.1.1.1.3 C: Combination C.1.1.1.3/B.2.2.3.… #> 5 AB12345 AB12345-BRA-11-id-8   dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.… #> 6 AB12345 AB12345-BRA-12-id-120 dcd C.1.1.1.3 A: Drug X      C.1.1.1.3/B.2.2.3.…"},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"Helper functions used internally STEP calculations.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"","code":"h_step_window(x, control = control_step())  h_step_trt_effect(data, model, variables, x)  h_step_survival_formula(variables, control = control_step())  h_step_survival_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_coxph() )  h_step_rsp_formula(variables, control = c(control_step(), control_logistic()))  h_step_rsp_est(   formula,   data,   variables,   x,   subset = rep(TRUE, nrow(data)),   control = control_logistic() )"},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"x (numeric) biomarker value(s) use (without NA). control (named list) output control_step(). data (data.frame) dataset containing variables summarize. model (coxph glm) regression model object. variables (named list string) list additional analysis variables. formula (formula) regression model formula. subset (logical) subset vector.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window() returns list containing window-selection matrix sel interval information matrix interval. h_step_trt_effect() returns vector elements est se. h_step_survival_formula() returns model formula. h_step_survival_est() returns matrix number observations n, events, log hazard ratio estimates loghr, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x. h_step_rsp_formula() returns model formula. h_step_rsp_est() returns matrix number observations n, log odds ratio estimates logor, standard error se, Wald confidence interval bounds ci_lower ci_upper. One row included biomarker value x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_step.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for subgroup treatment effect pattern (STEP) calculations — h_step","text":"h_step_window(): Creates windows STEP, based control settings provided. h_step_trt_effect(): Calculates estimated treatment effect estimate linear predictor scale corresponding standard error STEP model fitted data given variables specification, single biomarker value x. works coxph glm models, .e. calculating log hazard ratio log odds ratio estimates. h_step_survival_formula(): Builds model formula used survival STEP calculations. h_step_survival_est(): Estimates model formula built based variables data given subset control parameters Cox regression. h_step_rsp_formula(): Builds model formula used response STEP calculations. h_step_rsp_est(): Estimates model formula built based variables data given subset control parameters logistic regression.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"Helper functions documented separately confuse user reading user-facing functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"h_surv_to_coxreg_variables(variables, biomarker)  h_coxreg_mult_cont_df(variables, data, control = control_coxreg())  h_tab_surv_one_biomarker(   df,   vars,   time_unit,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"variables (named list string) list additional analysis variables. biomarker (string) name biomarker variable. data (data.frame) dataset containing variables summarize. control (list) list parameters returned helper function control_coxreg(). df (data.frame) results single biomarker, part returned extract_survival_biomarkers() (needs couple columns added high-level function relative returned h_coxreg_mult_cont_df(), see example). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables() returns named list elements time, event, arm, covariates, strata. h_coxreg_mult_cont_df() returns data.frame containing estimates statistics selected biomarkers. h_tab_surv_one_biomarker() returns rtables table object given statistics arranged columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"h_surv_to_coxreg_variables(): Helps converting \"survival\" function variable list \"Cox regression\" variable list. reason currently inconsistency variable names accepted extract_survival_subgroups() fit_coxreg_multivar(). h_coxreg_mult_cont_df(): Prepares estimates number events, patients median survival times, well hazard ratio estimates, confidence intervals p-values, multiple biomarkers given single data set. variables corresponds names variables found data, passed named list requires elements tte, is_event, biomarkers (vector continuous biomarker variables) optionally subgroups strata. h_tab_surv_one_biomarker(): Prepares single sub-table given df_sub containing results single biomarker.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating biomarker effects on survival by subgroup — h_survival_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte, fill = FALSE)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # This is how the variable list is converted internally. h_surv_to_coxreg_variables(   variables = list(     tte = \"AVAL\",     is_event = \"EVNT\",     covariates = c(\"A\", \"B\"),     strata = \"D\"   ),   biomarker = \"AGE\" ) #> $time #> [1] \"AVAL\" #>  #> $event #> [1] \"EVNT\" #>  #> $arm #> [1] \"AGE\" #>  #> $covariates #> [1] \"A\" \"B\" #>  #> $strata #> [1] \"D\" #>   # For a single population, estimate separately the effects # of two biomarkers. df <- h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median       hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.000189 #> 2       AGE                          Age   200          141 753.5176 1.008267 #>         lcl      ucl conf_level      pval     pval_label #> 1 0.9511092 1.051802       0.95 0.9941244 p-value (Wald) #> 2 0.9845155 1.032591       0.95 0.4984743 p-value (Wald)  # If the data set is empty, still the corresponding rows with missings are returned. h_coxreg_mult_cont_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"REGION1\",     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f[NULL, ] ) #>   biomarker              biomarker_label n_tot n_tot_events median hr lcl ucl #> 1    BMRKR1 Continuous Level Biomarker 1     0            0     NA NA  NA  NA #> 2       AGE                          Age     0            0     NA NA  NA  NA #>   conf_level pval     pval_label #> 1       0.95   NA p-value (Wald) #> 2       0.95   NA p-value (Wald)  # Starting from above `df`, zoom in on one biomarker and add required columns. df1 <- df[1, ] df1$subgroup <- \"All patients\" df1$row_type <- \"content\" df1$var <- \"ALL\" df1$var_label <- \"All patients\" h_tab_surv_one_biomarker(   df1,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   time_unit = \"days\" ) #>                Total n   Total Events   Median (days)   Hazard Ratio   95% Wald CI    p-value (Wald) #> ———————————————————————————————————————————————————————————————————————————————————————————————————— #> All patients     200         141            753.5           1.00       (0.95, 1.05)       0.9941"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Helper functions tabulate data frame statistics median survival time hazard ratio population subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"h_survtime_df(tte, is_event, arm)  h_survtime_subgroups_df(   variables,   data,   groups_lists = list(),   label_all = \"All Patients\" )  h_coxph_df(tte, is_event, arm, strata_data = NULL, control = control_coxph())  h_coxph_subgroups_df(   variables,   data,   groups_lists = list(),   control = control_coxph(),   label_all = \"All Patients\" )"},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"tte (numeric) vector time--event duration values. is_event (flag)TRUE event, FALSE time event censored. arm (factor) treatment group variable. variables (named list string) list additional analysis variables. data (data.frame) dataset containing variables summarize. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. strata_data (factor, data.frame, NULL) required stratified analysis performed. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df() returns data.frame columns arm, n, n_events, median. h_survtime_subgroups_df() returns data.frame columns arm, n, n_events, median, subgroup, var, var_label, row_type. h_coxph_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval pval_label. h_coxph_subgroups_df() returns data.frame columns arm, n_tot, n_tot_events, hr, lcl, ucl, conf_level, pval, pval_label, subgroup, var, var_label, row_type.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"Main functionality prepare data use layout-creating function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"h_survtime_df(): Helper prepare data frame median survival times arm. h_survtime_subgroups_df(): Summarizes median survival times arm across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups. groups_lists optionally specifies groupings subgroups variables. h_coxph_df(): Helper prepare data frame estimates treatment hazard ratio. h_coxph_subgroups_df(): Summarizes estimates treatment hazard ratio across subgroups data frame. variables corresponds names variables found data, passed named list requires elements tte, is_event, arm optionally subgroups strata. groups_lists optionally specifies groupings subgroups variables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for tabulating survival duration by subgroup — h_survival_duration_subgroups","text":"","code":"library(dplyr) library(forcats)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     is_event = CNSR == 0   ) labels <- c(\"ARM\" = adtte_labels[[\"ARM\"]], \"SEX\" = adtte_labels[[\"SEX\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Extract median survival time for one group. h_survtime_df(   tte = adtte_f$AVAL,   is_event = adtte_f$is_event,   arm = adtte_f$ARM ) #>          arm  n n_events   median #> 1 B: Placebo 73       57 727.8043 #> 2  A: Drug X 69       44 974.6402  # Extract median survival time for multiple groups. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>           arm  n n_events    median     subgroup    var #> 1  B: Placebo 73       57  727.8043 All Patients    ALL #> 2   A: Drug X 69       44  974.6402 All Patients    ALL #> 3  B: Placebo 40       31  599.1772            F    SEX #> 4   A: Drug X 38       24 1016.2982            F    SEX #> 5  B: Placebo 33       26  888.4916            M    SEX #> 6   A: Drug X 31       20  974.6402            M    SEX #> 7  B: Placebo 24       21  735.4722          LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402          LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352       MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197       MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245         HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Define groupings for BMRKR2 levels. h_survtime_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis  # Extract hazard ratio for one group. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM) #>   arm n_tot n_tot_events        hr       lcl      ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.057337       0.95 0.09049511 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for one group with stratification factor. h_coxph_df(adtte_f$AVAL, adtte_f$is_event, adtte_f$ARM, strata_data = adtte_f$STRATA1) #>   arm n_tot n_tot_events        hr       lcl     ucl conf_level       pval #> 1       142          101 0.6646586 0.4399495 1.00414       0.95 0.05089188 #>           pval_label #> 1 p-value (log-rank)  # Extract hazard ratio for multiple groups. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis  # Define groupings of BMRKR2 levels. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis  # Extract hazard ratio for multiple groups with stratification factors. h_coxph_subgroups_df(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\",     subgroups = c(\"SEX\", \"BMRKR2\"),     strata = c(\"STRATA1\", \"STRATA2\")   ),   data = adtte_f ) #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.6126133 0.3913507 0.9589739       0.95 0.03086774 #> 2        78           55 0.3934024 0.2027682 0.7632630       0.95 0.00469167 #> 3        64           46 0.9501768 0.4730073 1.9087145       0.95 0.88580522 #> 4        50           36 0.7378635 0.3140465 1.7336363       0.95 0.48408079 #> 5        49           31 0.9408062 0.4172095 2.1215148       0.95 0.88305965 #> 6        43           34 0.5125617 0.2125140 1.2362459       0.95 0.13124382 #>           pval_label     subgroup    var                    var_label row_type #> 1 p-value (log-rank) All Patients    ALL                 All Patients  content #> 2 p-value (log-rank)            F    SEX                          Sex analysis #> 3 p-value (log-rank)            M    SEX                          Sex analysis #> 4 p-value (log-rank)          LOW BMRKR2 Continuous Level Biomarker 2 analysis #> 5 p-value (log-rank)       MEDIUM BMRKR2 Continuous Level Biomarker 2 analysis #> 6 p-value (log-rank)         HIGH BMRKR2 Continuous Level Biomarker 2 analysis"},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"Please see h_tab_surv_one_biomarker() h_tab_rsp_one_biomarker(), use function examples. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"","code":"h_tab_one_biomarker(   df,   afuns,   colvars,   na_str = default_na_str(),   .indent_mods = 0L,   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"df (data.frame) results single biomarker. afuns (named list function) analysis functions. colvars (named list) named list elements vars (variables tabulate) labels (labels). na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tab_one_biomarker.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for tabulation of a single biomarker result — h_tab_one_biomarker","text":"rtables table object statistics columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"Create data.frame pairwise stratified unstratified Cox-PH analysis results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"h_tbl_coxph_pairwise(   df,   variables,   ref_group_coxph = NULL,   control_coxph_pw = control_coxph(),   annot_coxph_ref_lbls = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"df (data.frame) data set containing analysis variables. variables (named list) variable names. Details : tte (numeric) variable indicating time--event duration values. is_event (logical) event variable. TRUE event, FALSE time event censored. arm (factor) treatment group variable. strata (character NULL) variable names indicating stratification factors. ref_group_coxph (string NULL) level arm variable use reference group calculations annot_coxph table. NULL (default), uses first level arm variable. control_coxph_pw (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing hazard ratio = 1. Default method \"log-rank\", can also set \"wald\" \"likelihood\". ties (string) method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph() conf_level (proportion) confidence level interval HR. annot_coxph_ref_lbls (flag) whether reference group explicitly printed labels annot_coxph table. FALSE (default), comparison groups printed annot_coxph table labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"data.frame containing statistics HR, XX% CI (XX taken control_coxph_pw), p-value (log-rank).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for generating a pairwise Cox-PH table — h_tbl_coxph_pairwise","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  h_tbl_coxph_pairwise(   df = adtte,   variables = list(tte = \"AVAL\", is_event = \"is_event\", arm = \"ARM\"),   control_coxph_pw = control_coxph(conf_level = 0.9) ) #>                  HR       90% CI p-value (log-rank) #> B: Placebo     1.41 (1.01, 1.96)             0.0905 #> C: Combination 1.81 (1.24, 2.64)             0.0086"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for survival estimations — h_tbl_median_surv","title":"Helper function for survival estimations — h_tbl_median_surv","text":"Transform survival fit table groups rows characterized N, median confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"h_tbl_median_surv(fit_km, armval = \"All\")"},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for survival estimations — h_tbl_median_surv","text":"fit_km (survfit) result survival::survfit(). armval (string) used strata name treatment arm variable one level. Default \"\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for survival estimations — h_tbl_median_surv","text":"summary table statistics N, Median, XX% CI (XX taken fit_km).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_tbl_median_surv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for survival estimations — h_tbl_median_surv","text":"","code":"library(dplyr) library(survival)  adtte <- tern_ex_adtte %>% filter(PARAMCD == \"OS\") fit <- survfit(   formula = Surv(AVAL, 1 - CNSR) ~ ARMCD,   data = adtte ) h_tbl_median_surv(fit_km = fit) #>        N Median        95% CI #> ARM A 69  974.6   (687, 1625) #> ARM B 73  727.8 (555.8, 1156) #> ARM C 58  632.3   (393, 1001)"},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"Helper function count number patients fraction patients according highest post-baseline lab grade variable .var, baseline lab grade variable baseline_var, direction interest specified direction_var.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"h_worsen_counter(df, id, .var, baseline_var, direction_var)"},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"df (data.frame) data set containing analysis variables. id (string) subject variable name. .var (string) single variable name passed rtables requested statistics function. baseline_var (string) name baseline lab grade variable. direction_var (string) name direction variable specifying direction shift table interest. lab records flagged L, H B included shift table. L: low direction H: high direction B: low high directions","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"counts fraction patients whose worst post-baseline lab grades worse baseline grades, post-baseline worst grades \"1\", \"2\", \"3\", \"4\" \"\".","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/h_worsen_counter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to analyze patients for s_count_abnormal_lab_worsen_by_baseline() — h_worsen_counter","text":"","code":"library(dplyr)  # The direction variable, GRADDR, is based on metadata adlb <- tern_ex_adlb %>%   mutate(     GRADDR = case_when(       PARAMCD == \"ALT\" ~ \"B\",       PARAMCD == \"CRP\" ~ \"L\",       PARAMCD == \"IGA\" ~ \"H\"     )   ) %>%   filter(SAFFL == \"Y\" & ONTRTFL == \"Y\" & GRADDR != \"\")  df <- h_adlb_worsen(   adlb,   worst_flag_low = c(\"WGRLOFL\" = \"Y\"),   worst_flag_high = c(\"WGRHIFL\" = \"Y\"),   direction_var = \"GRADDR\" )  # `h_worsen_counter` h_worsen_counter(   df %>% filter(PARAMCD == \"CRP\" & GRADDR == \"Low\"),   id = \"USUBJID\",   .var = \"ATOXGR\",   baseline_var = \"BTOXGR\",   direction_var = \"GRADDR\" ) #> $fraction #> $fraction$`1` #>   num denom  #>    25   180  #>  #> $fraction$`2` #>   num denom  #>    15   186  #>  #> $fraction$`3` #>   num denom  #>    18   191  #>  #> $fraction$`4` #>   num denom  #>    17   196  #>  #> $fraction$Any #>   num denom  #>    75   196  #>  #>"},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function to calculate x-tick positions — h_xticks","title":"Helper function to calculate x-tick positions — h_xticks","text":"Calculate positions ticks x-axis. However, xticks already exists kept . based function ggplot2 relies , required graphic patient--risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"h_xticks(data, xticks = NULL, max_time = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function to calculate x-tick positions — h_xticks","text":"data (data.frame) survival data pre-processed h_data_plot. xticks (numeric NULL) numeric vector tick positions single number spacing ticks x-axis. NULL (default), labeling::extended() used determine optimal tick positions x-axis. max_time (numeric(1)) maximum value show x-axis. data values less threshold value plotted (defaults NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function to calculate x-tick positions — h_xticks","text":"vector positions use x-axis ticks ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/h_xticks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function to calculate x-tick positions — h_xticks","text":"","code":"library(dplyr) library(survival)  data <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   survfit(formula = Surv(AVAL, 1 - CNSR) ~ ARMCD, data = .) %>%   h_data_plot()  h_xticks(data) #> [1]    0 1000 2000 3000 4000 5000 h_xticks(data, xticks = seq(0, 3000, 500)) #> [1]    0  500 1000 1500 2000 2500 3000 h_xticks(data, xticks = 500) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 h_xticks(data, xticks = 500, max_time = 6000) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500 6000 h_xticks(data, xticks = c(0, 500), max_time = 300) #> [1]   0 500 h_xticks(data, xticks = 500, max_time = 300) #>  [1]    0  500 1000 1500 2000 2500 3000 3500 4000 4500"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"imputation_rule(   df,   x_stats,   stat,   imp_rule,   post = FALSE,   avalcat_var = \"AVALCAT1\" )"},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"df (data.frame) data set containing analysis variables. x_stats (named list) named list statistics, typically results s_summary(). stat (string) statistic return value/NA level according imputation rule applied. imp_rule (string) imputation rule setting. Set \"1/3\" implement 1/3 imputation rule \"1/2\" implement 1/2 imputation rule. post (flag) whether data corresponds post-dose time-point (defaults FALSE). parameter used imp_rule set \"1/3\". avalcat_var (string) name variable indicates whether row df corresponds analysis value category \"BLQ\", \"LTR\", \"<PCLLOQ\", none (defaults \"AVALCAT1\"). Variable avalcat_var must present df.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"list containing statistic value (val) NA level (na_str) displayed according specified imputation rule.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/imputation_rule.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply 1/3 or 1/2 imputation rule to data — imputation_rule","text":"","code":"set.seed(1) df <- data.frame(   AVAL = runif(50, 0, 1),   AVALCAT1 = sample(c(1, \"BLQ\"), 50, replace = TRUE) ) x_stats <- s_summary(df$AVAL) imputation_rule(df, x_stats, \"max\", \"1/3\") #> $val #>       max  #> 0.9919061  #>  #> $na_str #> [1] \"ND\" #>  imputation_rule(df, x_stats, \"geom_mean\", \"1/3\") #> $val #> [1] NA #>  #> $na_str #> [1] \"NE\" #>  imputation_rule(df, x_stats, \"mean\", \"1/2\") #> $val #> [1] NA #>  #> $na_str #> [1] \"ND\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence rate estimation — incidence_rate","title":"Incidence rate estimation — incidence_rate","text":"analyze function estimate_incidence_rate() creates layout element estimate event rate adjusted person-years risk, otherwise known incidence rate. primary analysis variable specified via vars person-years risk. addition variable, n_events variable number events observed (value 1 means event observed 0 means event observed) must also specified.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence rate estimation — incidence_rate","text":"","code":"estimate_incidence_rate(   lyt,   vars,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   na_str = default_na_str(),   nested = TRUE,   summarize = FALSE,   label_fmt = \"%s - %.labels\",   ...,   show_labels = \"hidden\",   table_names = vars,   .stats = c(\"person_years\", \"n_events\", \"rate\", \"rate_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_incidence_rate(   df,   .var,   n_events,   is_event = lifecycle::deprecated(),   id_var = \"USUBJID\",   control = control_incidence_rate() )  a_incidence_rate(   df,   labelstr = \"\",   .var,   .df_row,   n_events,   id_var = \"USUBJID\",   control = control_incidence_rate(),   .stats = NULL,   .formats = c(person_years = \"xx.x\", n_events = \"xx\", rate = \"xx.xx\", rate_ci =     \"(xx.xx, xx.xx)\", n_unique = \"xx\", n_rate = \"xx (xx.x)\"),   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str(),   label_fmt = \"%s - %.labels\" )"},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence rate estimation — incidence_rate","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . n_events (string) name integer variable indicating whether event observed (1) (0). id_var (string) name variable used patient identifier \"n_unique\" included .stats. Defaults \"USUBJID\". control (list) parameters estimation details, specified using helper function control_incidence_rate(). Possible parameter options : conf_level (proportion) confidence level estimated incidence rate. conf_type (string)normal (default), normal_log, exact, byar confidence interval type. input_time_unit (string)day, week, month, year (default) indicating time unit data input. num_pt_year (numeric) time unit desired output (person-years). na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. summarize (flag) whether function act analyze function (summarize = FALSE), summarize function (summarize = TRUE). Defaults FALSE. label_fmt (string) labels formatted row split occurs summarize = TRUE. string use \"%s\" represent row split levels, \"%.labels\" represent labels supplied .labels argument. Defaults \"%s - %.labels\". ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'person_years', 'n_events', 'rate', 'rate_ci', 'n_unique', 'n_rate' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_incidence_rate() table layout. s_incidence_rate() returns following statistics: person_years: Total person-years risk. n_events: Total number events observed. rate: Estimated incidence rate. rate_ci: Confidence interval incidence rate. n_unique: Total number patients least one event observed. n_rate: Total number events observed & estimated incidence rate. a_incidence_rate() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Incidence rate estimation — incidence_rate","text":"estimate_incidence_rate(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_incidence_rate(): Statistics function estimates incidence rate associated confidence interval. a_incidence_rate(): Formatted analysis function used afun estimate_incidence_rate().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/incidence_rate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence rate estimation — incidence_rate","text":"","code":"df <- data.frame(   USUBJID = as.character(seq(6)),   CNSR = c(0, 1, 1, 0, 0, 0),   AVAL = c(10.1, 20.4, 15.3, 20.8, 18.7, 23.4),   ARM = factor(c(\"A\", \"A\", \"A\", \"B\", \"B\", \"B\")),   STRATA1 = factor(c(\"X\", \"Y\", \"Y\", \"X\", \"X\", \"Y\")) ) df$n_events <- 1 - df$CNSR  basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     control = control_incidence_rate(       input_time_unit = \"month\",       num_pt_year = 100     )   ) %>%   build_table(df) #>                                            A                 B        #>                                          (N=3)             (N=3)      #> ————————————————————————————————————————————————————————————————————— #> Total patient-years at risk               3.8               5.2       #> Number of adverse events observed          1                 3        #> AE rate per 100 patient-years            26.20             57.23      #> 95% CI                              (-25.15, 77.55)   (-7.53, 122.00)  # summarize = TRUE basic_table(show_colcounts = TRUE) %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"STRATA1\", child_labels = \"visible\") %>%   estimate_incidence_rate(     vars = \"AVAL\",     n_events = \"n_events\",     .stats = c(\"n_unique\", \"n_rate\"),     summarize = TRUE,     label_fmt = \"%.labels\"   ) %>%   build_table(df) #>                                                                          A         B    #>                                                                        (N=3)     (N=3)  #> ——————————————————————————————————————————————————————————————————————————————————————— #> X                                                                                       #>   Total number of patients with at least one adverse event               1         2    #>   Number of adverse events observed (AE rate per 100 patient-years)   1 (9.9)   2 (5.1) #> Y                                                                                       #>   Total number of patients with at least one adverse event               0         1    #>   Number of adverse events observed (AE rate per 100 patient-years)   0 (0.0)   1 (4.3)  a_incidence_rate(   df,   .var = \"AVAL\",   .df_row = df,   n_events = \"n_events\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>       row_name formatted_cell indent_mod #> 1 person_years          108.7          0 #> 2     n_events              4          0 #> 3         rate           3.68          0 #> 4      rate_ci   (0.07, 7.29)          0 #> 5     n_unique              4          0 #> 6       n_rate        4 (3.7)          0 #>                                                           row_label #> 1                                       Total patient-years at risk #> 2                                 Number of adverse events observed #> 3                                     AE rate per 100 patient-years #> 4                                                            95% CI #> 5          Total number of patients with at least one adverse event #> 6 Number of adverse events observed (AE rate per 100 patient-years)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Labels or names of list elements — labels_or_names","title":"Labels or names of list elements — labels_or_names","text":"Internal helper function working nested statistic function results typically labels names can use.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Labels or names of list elements — labels_or_names","text":"","code":"labels_or_names(x)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Labels or names of list elements — labels_or_names","text":"x (list) list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_or_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Labels or names of list elements — labels_or_names","text":"character vector labels names list elements.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":null,"dir":"Reference","previous_headings":"","what":"Update labels according to control specifications — labels_use_control","title":"Update labels according to control specifications — labels_use_control","text":"Given list statistic labels list control parameters, updates labels relevant control specification. example, control element conf_level set 0.9, default label statistic mean_ci updated \"Mean 90% CI\". labels supplied via labels_custom updated regardless control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update labels according to control specifications — labels_use_control","text":"","code":"labels_use_control(labels_default, control, labels_custom = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update labels according to control specifications — labels_use_control","text":"labels_default (named character) named vector statistic labels modify according control specifications. Labels explicitly defined labels_custom affected. control (named list) list control parameters apply adjust default labels. labels_custom (named character) named vector labels customized user affected control.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update labels according to control specifications — labels_use_control","text":"named character vector labels control specifications applied relevant labels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/labels_use_control.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update labels according to control specifications — labels_use_control","text":"","code":"control <- list(conf_level = 0.80, quantiles = c(0.1, 0.83), test_mean = 0.57) get_labels_from_stats(c(\"mean_ci\", \"quantiles\", \"mean_pval\")) %>%   labels_use_control(control = control) #>                          mean_ci                        quantiles  #>                    \"Mean 80% CI\"                \"10% and 83%-ile\"  #>                        mean_pval  #> \"Mean p-value (H0: mean = 0.57)\""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression multivariate column layout function — logistic_regression_cols","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"Layout-creating function creates multivariate column layout summarizing logistic regression results. function wrapper rtables::split_cols_by_multivar().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"","code":"logistic_regression_cols(lyt, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_regression_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression multivariate column layout function — logistic_regression_cols","text":"layout object suitable passing layouting functions. Adding function rtable layout split table columns corresponding statistics df, estimate, std_error, odds_ratio, ci, pvalue.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic regression summary table — logistic_summary_by_flag","title":"Logistic regression summary table — logistic_summary_by_flag","text":"Constructor content functions used summarize_logistic() summarize logistic regression results. function wrapper rtables::summarize_row_groups().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic regression summary table — logistic_summary_by_flag","text":"","code":"logistic_summary_by_flag(   flag_var,   na_str = default_na_str(),   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic regression summary table — logistic_summary_by_flag","text":"flag_var (string) variable name identifying row used content function. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/logistic_summary_by_flag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic regression summary table — logistic_summary_by_flag","text":"content function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":null,"dir":"Reference","previous_headings":"","what":"Make names without dots — make_names","title":"Make names without dots — make_names","text":"Make names without dots","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make names without dots — make_names","text":"","code":"make_names(nams)"},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make names without dots — make_names","text":"nams (character) vector original names.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/make_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make names without dots — make_names","text":"character vector proper names, use dots contrast make.names().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":null,"dir":"Reference","previous_headings":"","what":"Conversion of months to days — month2day","title":"Conversion of months to days — month2day","text":"Conversion months days. approximative calculation considers month average 30.4375 days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Conversion of months to days — month2day","text":"","code":"month2day(x)"},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Conversion of months to days — month2day","text":"x (numeric(1)) time months.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Conversion of months to days — month2day","text":"numeric vector time days.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/month2day.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Conversion of months to days — month2day","text":"","code":"x <- c(13.25, 8.15, 1, 2.834) month2day(x) #> [1] 403.29688 248.06563  30.43750  86.25988"},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"Muffled car::Anova — muffled_car_anova","title":"Muffled car::Anova — muffled_car_anova","text":"Applied survival models, car::Anova() signal strata terms dropped model formula present, function deliberately muffles message.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Muffled car::Anova — muffled_car_anova","text":"","code":"muffled_car_anova(mod, test_statistic)"},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Muffled car::Anova — muffled_car_anova","text":"mod (coxph) Cox regression model fitted survival::coxph(). test_statistic (string) method used estimation p.values; wald (default) likelihood.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/muffled_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Muffled car::Anova — muffled_car_anova","text":"output car::Anova(), convergence message muffled.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of available (non-missing entries) in a vector — n_available","title":"Number of available (non-missing entries) in a vector — n_available","text":"Small utility function better readability.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of available (non-missing entries) in a vector — n_available","text":"","code":"n_available(x)"},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of available (non-missing entries) in a vector — n_available","text":"x (vector) vector count non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/n_available.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of available (non-missing entries) in a vector — n_available","text":"Number non-missing values.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":null,"dir":"Reference","previous_headings":"","what":"Odds ratio estimation — odds_ratio","title":"Odds ratio estimation — odds_ratio","text":"analyze function estimate_odds_ratio() creates layout element compare bivariate responses two groups estimating odds ratio confidence interval. primary analysis variable specified vars group variable. Additional variables can included analysis via variables argument, accepts arm, arm variable, strata, stratification variable. two arm levels present, can combined two groups using groups_list argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Odds ratio estimation — odds_ratio","text":"","code":"estimate_odds_ratio(   lyt,   vars,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   na_str = default_na_str(),   nested = TRUE,   method = \"exact\",   show_labels = \"hidden\",   table_names = vars,   var_labels = vars,   .stats = \"or_ci\",   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )  a_odds_ratio(   df,   .var,   .ref_group,   .in_ref_col,   .df_row,   variables = list(arm = NULL, strata = NULL),   conf_level = 0.95,   groups_list = NULL,   method = \"exact\" )"},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Odds ratio estimation — odds_ratio","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. method (string) whether use correct (\"exact\") calculation conditional likelihood one approximations. See survival::clogit() details. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. var_labels (character) variable labels. .stats (character) statistics select table. Options : 'or_ci', 'n_tot' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_odds_ratio() table layout. s_odds_ratio() returns named list statistics or_ci (containing est, lcl, ucl) n_tot. a_odds_ratio() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Odds ratio estimation — odds_ratio","text":"estimate_odds_ratio(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_odds_ratio(): Statistics function estimates odds ratio treatment control. variables list arm strata variable names must passed stratified analysis required. a_odds_ratio(): Formatted analysis function used afun estimate_odds_ratio().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Odds ratio estimation — odds_ratio","text":"function uses logistic regression unstratified analyses, conditional logistic regression stratified analyses. Wald confidence interval calculated specified confidence level. stratified analyses, currently implementation conditional likelihood confidence intervals, therefore likelihood confidence interval available option. vars contains responders non-responders odds ratio estimation possible returned values NA.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/odds_ratio.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Odds ratio estimation — odds_ratio","text":"","code":"set.seed(12) dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50), levels = c(\"A\", \"B\")),   strata = factor(sample(c(\"C\", \"D\"), 100, TRUE)) )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_odds_ratio(vars = \"rsp\")  build_table(l, df = dta) #>                               A            B #> ———————————————————————————————————————————— #> Odds Ratio (95% CI)   0.85 (0.38 - 1.88)      # Unstratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> $or_ci #>       est       lcl       ucl  #> 0.8484848 0.3831831 1.8788053  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   # Stratified analysis. s_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta,   variables = list(arm = \"grp\", strata = \"strata\") ) #> $or_ci #>       est       lcl       ucl  #> 0.7689750 0.3424155 1.7269154  #> attr(,\"label\") #> [1] \"Odds Ratio (95% CI)\" #>  #> $n_tot #> n_tot  #>   100  #> attr(,\"label\") #> [1] \"Total n\" #>   a_odds_ratio(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   .df_row = dta ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name     formatted_cell indent_mod           row_label #> 1    or_ci 0.85 (0.38 - 1.88)          1 Odds Ratio (95% CI) #> 2    n_tot                100          0             Total n"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference estimation — prop_diff","title":"Proportion difference estimation — prop_diff","text":"analysis function estimate_proportion_diff() creates layout element estimate difference proportion responders within studied population. primary analysis variable, vars, logical variable indicating whether response occurred record. See method parameter options methods use constructing confidence interval proportion difference. stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference estimation — prop_diff","text":"","code":"estimate_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\",   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )  a_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   conf_level = 0.95,   method = c(\"waldcc\", \"wald\", \"cmh\", \"ha\", \"newcombe\", \"newcombecc\", \"strat_newcombe\",     \"strat_newcombecc\"),   weights_method = \"cmh\" )"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference estimation — prop_diff","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. conf_level (proportion) confidence level interval. method (string) method used confidence interval estimation. weights_method (string) weights method. Can either \"cmh\" \"heuristic\" directs way weights estimated. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'diff', 'diff_ci' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_proportion_diff() table layout. s_proportion_diff() returns named list elements diff diff_ci. a_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Proportion difference estimation — prop_diff","text":"estimate_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_proportion_diff(): Statistics function estimating difference terms responder proportion. a_proportion_diff(): Formatted analysis function used afun estimate_proportion_diff().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Proportion difference estimation — prop_diff","text":"performing unstratified analysis, methods \"cmh\", \"strat_newcombe\", \"strat_newcombecc\" permitted.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference estimation — prop_diff","text":"","code":"## \"Mid\" case: 4/4 respond in group A, 1/2 respond in group B. nex <- 100 # Number of example rows dta <- data.frame(   \"rsp\" = sample(c(TRUE, FALSE), nex, TRUE),   \"grp\" = sample(c(\"A\", \"B\"), nex, TRUE),   \"f1\" = sample(c(\"a1\", \"a2\"), nex, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), nex, TRUE),   stringsAsFactors = TRUE )  l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   estimate_proportion_diff(     vars = \"rsp\",     conf_level = 0.90,     method = \"ha\"   )  build_table(l, df = dta) #>                                        A         B #> —————————————————————————————————————————————————— #> Difference in Response rate (%)       12.0         #>   90% CI (Anderson-Hauck)         (-5.4, 29.4)      s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> $diff #> [1] 12 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -5.374519 29.374519 #> attr(,\"label\") #> [1] \"90% CI (Anderson-Hauck)\" #>   # CMH example with strata s_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   variables = list(strata = c(\"f1\", \"f2\")),   conf_level = 0.90,   method = \"cmh\" ) #> $diff #> [1] 12.05847 #> attr(,\"label\") #> [1] \"Difference in Response rate (%)\" #>  #> $diff_ci #> [1] -2.67057 26.78750 #> attr(,\"label\") #> [1] \"90% CI (CMH, without correction)\" #>   a_proportion_diff(   df = subset(dta, grp == \"A\"),   .var = \"rsp\",   .ref_group = subset(dta, grp == \"B\"),   .in_ref_col = FALSE,   conf_level = 0.90,   method = \"ha\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod                       row_label #> 1     diff           12.0          0 Difference in Response rate (%) #> 2  diff_ci   (-5.4, 29.4)          1         90% CI (Anderson-Hauck)"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":null,"dir":"Reference","previous_headings":"","what":"Difference test for two proportions — prop_diff_test","title":"Difference test for two proportions — prop_diff_test","text":"analyze function test_proportion_diff() creates layout element test difference two proportions. primary analysis variable, vars, indicates whether response occurred record. See method parameter options methods use calculate p-value. Additionally, stratification variable can supplied via strata element variables argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Difference test for two proportions — prop_diff_test","text":"","code":"test_proportion_diff(   lyt,   vars,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\"),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = vars,   show_labels = \"hidden\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )  a_test_proportion_diff(   df,   .var,   .ref_group,   .in_ref_col,   variables = list(strata = NULL),   method = c(\"chisq\", \"schouten\", \"fisher\", \"cmh\") )"},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Difference test for two proportions — prop_diff_test","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. method (string) one chisq, cmh, fisher, schouten; specifies test used calculate p-value. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_test_proportion_diff() table layout. s_test_proportion_diff() returns named list single item pval attribute label describing method used. p-value tests null hypothesis proportions two groups . a_test_proportion_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Difference test for two proportions — prop_diff_test","text":"test_proportion_diff(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_test_proportion_diff(): Statistics function tests difference two proportions. a_test_proportion_diff(): Formatted analysis function used afun test_proportion_diff().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/prop_diff_test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Difference test for two proportions — prop_diff_test","text":"","code":"dta <- data.frame(   rsp = sample(c(TRUE, FALSE), 100, TRUE),   grp = factor(rep(c(\"A\", \"B\"), each = 50)),   strata = factor(rep(c(\"V\", \"W\", \"X\", \"Y\", \"Z\"), each = 20)) )  # With `rtables` pipelines. l <- basic_table() %>%   split_cols_by(var = \"grp\", ref_group = \"B\") %>%   test_proportion_diff(     vars = \"rsp\",     method = \"cmh\", variables = list(strata = \"strata\")   )  build_table(l, df = dta) #>                                              A      B #> ————————————————————————————————————————————————————— #>   p-value (Cochran-Mantel-Haenszel Test)   1.0000"},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table pruning — prune_occurrences","title":"Occurrence table pruning — prune_occurrences","text":"Family constructor condition functions flexibly prune occurrence tables. condition functions always return whether row result higher threshold. Since class CombinationFunction() can logically combined condition functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table pruning — prune_occurrences","text":"","code":"keep_rows(row_condition)  keep_content_rows(content_row_condition)  has_count_in_cols(atleast, ...)  has_count_in_any_col(atleast, ...)  has_fraction_in_cols(atleast, ...)  has_fraction_in_any_col(atleast, ...)  has_fractions_difference(atleast, ...)  has_counts_difference(atleast, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table pruning — prune_occurrences","text":"row_condition (CombinationFunction) condition function works individual analysis rows flags whether kept pruned table. content_row_condition (CombinationFunction) condition function works individual first content rows leaf tables flags whether leaf tables kept pruned table. atleast (numeric(1)) threshold met order keep row. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows() returns pruning function can used rtables::prune_table() prune rtables table. keep_content_rows() returns pruning function checks condition first content row leaf tables table. has_count_in_cols() returns condition function sums counts specified column. has_count_in_any_col() returns condition function compares counts specified columns threshold. has_fraction_in_cols() returns condition function sums counts specified column, computes fraction dividing total column counts. has_fraction_in_any_col() returns condition function looks fractions specified columns checks whether fulfill threshold. has_fractions_difference() returns condition function extracts fractions specified column, computes difference minimum maximum. has_counts_difference() returns condition function extracts counts specified column, computes difference minimum maximum.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table pruning — prune_occurrences","text":"keep_rows(): Constructor creating pruning functions based row condition function. removes analysis rows (TableRow) pruned, .e., fulfill row condition. removes sub-tree children left. keep_content_rows(): Constructor creating pruning functions based condition (first) content row leaf tables. removes leaf tables first content row fulfill condition. check individual rows. proceeds recursively removing sub tree children left. has_count_in_cols(): Constructor creating condition functions total counts specified columns. has_count_in_any_col(): Constructor creating condition functions counts specified columns satisfying threshold. has_fraction_in_cols(): Constructor creating condition functions total fraction specified columns. has_fraction_in_any_col(): Constructor creating condition functions fraction specified columns. has_fractions_difference(): Constructor creating condition function checks difference fractions reported specified column. has_counts_difference(): Constructor creating condition function checks difference counts reported specified column.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Occurrence table pruning — prune_occurrences","text":"Since table specifications worded positively, name constructor condition functions positively, . However, note result keep_rows() says pruned, conform rtables::prune_table() interface.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/prune_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table pruning — prune_occurrences","text":"","code":"# \\donttest{ tab <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   split_rows_by(\"STRATA1\") %>%   summarize_row_groups() %>%   analyze_vars(\"COUNTRY\", .stats = \"count_fraction\") %>%   build_table(DM) # }  # \\donttest{ # `keep_rows` is_non_empty <- !CombinationFunction(all_zero_or_na) prune_table(tab, keep_rows(is_non_empty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # `keep_content_rows` # \\donttest{ more_than_twenty <- has_count_in_cols(atleast = 20L, col_names = names(tab)) prune_table(tab, keep_content_rows(more_than_twenty)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>     CHE                         0            0              0        #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     RUS                         0            0              0        #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     NGA                         0            0              0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>     CHE                         0            0              0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #>     JPN                         0            0              0        #>     GBR                         0            0              0        #>     CAN                         0            0              0        #>     CHE                         0            0              0        # }  # \\donttest{ more_than_one <- has_count_in_cols(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_count_in_any_col` any_more_than_one <- has_count_in_any_col(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(any_more_than_one)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fraction_in_cols` more_than_five_percent <- has_fraction_in_cols(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #> BLACK OR AFRICAN AMERICAN                                            #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    # }  # \\donttest{ # `has_fraction_in_any_col` any_atleast_five_percent <- has_fraction_in_any_col(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(any_atleast_five_percent)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ # `has_fractions_difference` more_than_five_percent_diff <- has_fractions_difference(atleast = 0.05, col_names = names(tab)) prune_table(tab, keep_rows(more_than_five_percent_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     PAK                      1 (8.3%)     1 (9.1%)      1 (14.3%)    #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }  # \\donttest{ more_than_one_diff <- has_counts_difference(atleast = 1L, col_names = names(tab)) prune_table(tab, keep_rows(more_than_one_diff)) #>                             A: Drug X    B: Placebo   C: Combination #> ———————————————————————————————————————————————————————————————————— #> ASIAN                                                                #>   A                         27 (22.3%)   20 (18.9%)     31 (24.0%)   #>     CHN                     14 (51.9%)    9 (45%)       12 (38.7%)   #>     USA                      2 (7.4%)      1 (5%)       8 (25.8%)    #>     BRA                      1 (3.7%)     4 (20%)        1 (3.2%)    #>     PAK                     3 (11.1%)     2 (10%)        2 (6.5%)    #>     NGA                     3 (11.1%)      1 (5%)        3 (9.7%)    #>     RUS                      2 (7.4%)      1 (5%)        1 (3.2%)    #>     JPN                         0          1 (5%)        2 (6.5%)    #>     GBR                         0          1 (5%)        1 (3.2%)    #>     CAN                      2 (7.4%)        0           1 (3.2%)    #>   B                         24 (19.8%)   29 (27.4%)     22 (17.1%)   #>     CHN                      12 (50%)    13 (44.8%)      11 (50%)    #>     USA                      2 (8.3%)    5 (17.2%)       1 (4.5%)    #>     BRA                     4 (16.7%)    3 (10.3%)       1 (4.5%)    #>     PAK                      2 (8.3%)     2 (6.9%)      4 (18.2%)    #>     NGA                      2 (8.3%)     1 (3.4%)      3 (13.6%)    #>     RUS                      1 (4.2%)     1 (3.4%)       2 (9.1%)    #>     JPN                         0        4 (13.8%)          0        #>     GBR                      1 (4.2%)        0              0        #>   C                         28 (23.1%)   19 (17.9%)     31 (24.0%)   #>     CHN                     13 (46.4%)   10 (52.6%)     16 (51.6%)   #>     USA                     3 (10.7%)    3 (15.8%)      4 (12.9%)    #>     BRA                      1 (3.6%)     1 (5.3%)      4 (12.9%)    #>     PAK                      1 (3.6%)     1 (5.3%)       3 (9.7%)    #>     NGA                     4 (14.3%)     1 (5.3%)       2 (6.5%)    #>     RUS                     4 (14.3%)    2 (10.5%)       1 (3.2%)    #>     JPN                      2 (7.1%)     1 (5.3%)       1 (3.2%)    #> BLACK OR AFRICAN AMERICAN                                            #>   A                          6 (5.0%)     7 (6.6%)       8 (6.2%)    #>     CHN                      3 (50%)     3 (42.9%)      5 (62.5%)    #>     USA                     2 (33.3%)    1 (14.3%)      1 (12.5%)    #>     BRA                         0        1 (14.3%)          0        #>     PAK                         0            0          1 (12.5%)    #>     NGA                         0            0          1 (12.5%)    #>     JPN                     1 (16.7%)        0              0        #>     GBR                         0        2 (28.6%)          0        #>   B                         10 (8.3%)     6 (5.7%)      12 (9.3%)    #>     CHN                      3 (30%)     2 (33.3%)      8 (66.7%)    #>     USA                      1 (10%)         0           1 (8.3%)    #>     BRA                      2 (20%)     1 (16.7%)       1 (8.3%)    #>     PAK                         0        1 (16.7%)          0        #>     RUS                         0        1 (16.7%)          0        #>     JPN                      2 (20%)         0           1 (8.3%)    #>     GBR                      1 (10%)         0           1 (8.3%)    #>     CAN                      1 (10%)     1 (16.7%)          0        #>   C                         12 (9.9%)    11 (10.4%)      7 (5.4%)    #>     CHN                     8 (66.7%)    5 (45.5%)      5 (71.4%)    #>     USA                      1 (8.3%)    2 (18.2%)      1 (14.3%)    #>     BRA                      1 (8.3%)    2 (18.2%)          0        #>     NGA                         0         1 (9.1%)          0        #>     RUS                      1 (8.3%)        0              0        #> WHITE                                                                #>   A                          3 (2.5%)     6 (5.7%)       6 (4.7%)    #>     CHN                     2 (66.7%)    2 (33.3%)       3 (50%)     #>     USA                     1 (33.3%)    1 (16.7%)          0        #>     PAK                         0        1 (16.7%)      1 (16.7%)    #>     NGA                         0        1 (16.7%)          0        #>     RUS                         0            0          1 (16.7%)    #>     JPN                         0        1 (16.7%)          0        #>     CAN                         0            0          1 (16.7%)    #>   B                          7 (5.8%)     5 (4.7%)       4 (3.1%)    #>     CHN                     4 (57.1%)     1 (20%)        3 (75%)     #>     USA                         0         1 (20%)           0        #>     BRA                         0         1 (20%)           0        #>     PAK                     1 (14.3%)        0              0        #>     NGA                     1 (14.3%)        0              0        #>     RUS                     1 (14.3%)        0           1 (25%)     #>     JPN                         0         1 (20%)           0        #>     CAN                         0         1 (20%)           0        #>   C                          4 (3.3%)     3 (2.8%)       8 (6.2%)    #>     CHN                      3 (75%)      3 (100%)       6 (75%)     #>     USA                      1 (25%)         0          1 (12.5%)    #>     JPN                         0            0          1 (12.5%)    # }"},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":null,"dir":"Reference","previous_headings":"","what":"Re-implemented range() default S3 method for numerical objects — range_noinf","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"function returns c(NA, NA) instead c(-Inf, Inf) zero-length data without warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"","code":"range_noinf(x, na.rm = FALSE, finite = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"x (numeric) sequence numbers range computed. na.rm (flag) flag indicating NA omitted. finite (flag) flag indicating non-finite elements removed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/range_noinf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Re-implemented range() default S3 method for numerical objects — range_noinf","text":"2-element vector class numeric.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":null,"dir":"Reference","previous_headings":"","what":"Reapply variable labels — reapply_varlabels","title":"Reapply variable labels — reapply_varlabels","text":"helper function used tests.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reapply variable labels — reapply_varlabels","text":"","code":"reapply_varlabels(x, varlabels, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reapply variable labels — reapply_varlabels","text":"x (vector) vector elements needs new labels. varlabels (character) vector labels x. ... parameters added list.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/reapply_varlabels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reapply variable labels — reapply_varlabels","text":"x variable labels reapplied.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"tabulate_rsp_biomarkers() function creates layout element tabulate estimated biomarker effects binary response endpoint across subgroups, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"tabulate_rsp_biomarkers(   df,   vars = c(\"n_tot\", \"n_rsp\", \"prop\", \"or\", \"ci\", \"pval\"),   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_rsp_biomarkers(). vars (character) names statistics reported among: n_tot: Total number patients per group. n_rsp: Total number responses per group. prop: Total response proportion per group. : Odds ratio. ci: Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, ci required. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"rtables table summarizing biomarker effects binary response subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"contrast tabulate_rsp_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/response_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on binary response by subgroup — response_biomarkers_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   mutate(rsp = AVALC == \"CR\") formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  df <- extract_rsp_biomarkers(   variables = list(     rsp = \"rsp\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adrs_f )  # \\donttest{ ## Table with default columns. tabulate_rsp_biomarkers(df) #>                                  Total n   Responders   Response (%)   Odds Ratio      95% CI      p-value (Wald) #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                               #>   All Patients                     200        164          82.0%          1.00      (0.95, 1.05)       0.8530     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          0.93      (0.85, 1.01)       0.0845     #>     MEDIUM                         68          58          85.3%          0.99      (0.88, 1.11)       0.8190     #>     HIGH                           62          53          85.5%          1.06      (0.96, 1.18)       0.2419     #> Continuous Level Biomarker 1                                                                                      #>   All Patients                     200        164          82.0%          0.98      (0.88, 1.08)       0.6353     #>   Continuous Level Biomarker 2                                                                                    #>     LOW                            70          53          75.7%          1.15      (0.95, 1.40)       0.1584     #>     MEDIUM                         68          58          85.3%          0.88      (0.73, 1.06)       0.1700     #>     HIGH                           62          53          85.5%          0.88      (0.72, 1.08)       0.2104      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_rsp_biomarkers(   df = df,   vars = c(\"n_rsp\", \"ci\", \"n_tot\", \"prop\", \"or\") )  ## Finally produce the forest plot. g_forest(tab, xlim = c(0.7, 1.4))  # }"},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate binary response by subgroup — response_subgroups","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups() function creates layout element tabulate binary response subgroup, returning statistics including response rate odds ratio population subgroup. table created df, list data frames returned extract_rsp_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"tabulate_rsp_subgroups(   lyt,   df,   vars = c(\"n_tot\", \"n\", \"prop\", \"or\", \"ci\"),   groups_lists = list(),   label_all = \"All Patients\",   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\") )  a_response_subgroups(   .formats = list(n = \"xx\", n_rsp = \"xx\", prop = \"xx.x%\", n_tot = \"xx\", or =     list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)), pval =     \"x.xxxx | (<0.0001)\", riskdiff = \"xx.x (xx.x - xx.x)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate binary response by subgroup — response_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_rsp_subgroups(). vars (character) names statistics reported among: n: Total number observations per group. n_rsp: Number responders per group. prop: Proportion responders. n_tot: Total number observations. : Odds ratio. ci : Confidence interval odds ratio. pval: p-value effect. Note, statistics n_tot, , ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all (string) label total population analysis. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$prop$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate binary response by subgroup — response_subgroups","text":"rtables table summarizing binary response subgroup. a_response_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate binary response by subgroup — response_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate binary response by subgroup — response_subgroups","text":"tabulate_rsp_subgroups(): Table-creating function creates table summarizing binary response subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_response_subgroups(): Formatted analysis function used afun tabulate_rsp_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/response_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate binary response by subgroup — response_subgroups","text":"","code":"library(dplyr) library(forcats)  adrs <- tern_ex_adrs adrs_labels <- formatters::var_labels(adrs)  adrs_f <- adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(ARM %in% c(\"A: Drug X\", \"B: Placebo\")) %>%   droplevels() %>%   mutate(     # Reorder levels of factor to make the placebo group the reference arm.     ARM = fct_relevel(ARM, \"B: Placebo\"),     rsp = AVALC == \"CR\"   ) formatters::var_labels(adrs_f) <- c(adrs_labels, \"Response\")  # Unstratified analysis. df <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f ) df #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142  2.714000 1.1804488  6.239827       0.95 All Patients    ALL #> 2        78 10.800000 2.2669576 51.452218       0.95            F    SEX #> 3        64  0.920000 0.2966470  2.853223       0.95            M    SEX #> 4        50  3.553846 1.0047370 12.570277       0.95          LOW BMRKR2 #> 5        49  2.705882 0.5911718 12.385232       0.95       MEDIUM BMRKR2 #> 6        43  2.250000 0.3970298 12.750933       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Stratified analysis. df_strat <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\"), strata = \"STRATA1\"),   data = adrs_f ) df_strat #> $prop #>           arm  n n_rsp      prop     subgroup    var #> 1  B: Placebo 73    50 0.6849315 All Patients    ALL #> 2   A: Drug X 69    59 0.8550725 All Patients    ALL #> 3  B: Placebo 40    25 0.6250000            F    SEX #> 4   A: Drug X 38    36 0.9473684            F    SEX #> 5  B: Placebo 33    25 0.7575758            M    SEX #> 6   A: Drug X 31    23 0.7419355            M    SEX #> 7  B: Placebo 24    13 0.5416667          LOW BMRKR2 #> 8   A: Drug X 26    21 0.8076923          LOW BMRKR2 #> 9  B: Placebo 23    17 0.7391304       MEDIUM BMRKR2 #> 10  A: Drug X 26    23 0.8846154       MEDIUM BMRKR2 #> 11 B: Placebo 26    20 0.7692308         HIGH BMRKR2 #> 12  A: Drug X 17    15 0.8823529         HIGH BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or       lcl       ucl conf_level     subgroup    var #> 1       142 2.6343899 1.1537821  6.015009       0.95 All Patients    ALL #> 2        78 9.5946605 2.0379337 45.171985       0.95            F    SEX #> 3        64 0.8947158 0.2936803  2.725809       0.95            M    SEX #> 4        50 3.5976656 1.0101319 12.813374       0.95          LOW BMRKR2 #> 5        49 2.6242168 0.5162572 13.339308       0.95       MEDIUM BMRKR2 #> 6        43 2.2816865 0.4116391 12.647228       0.95         HIGH BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Grouping of the BMRKR2 levels. df_grouped <- extract_rsp_subgroups(   variables = list(rsp = \"rsp\", arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")),   data = adrs_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $prop #>           arm  n n_rsp      prop        subgroup    var #> 1  B: Placebo 73    50 0.6849315    All Patients    ALL #> 2   A: Drug X 69    59 0.8550725    All Patients    ALL #> 3  B: Placebo 40    25 0.6250000               F    SEX #> 4   A: Drug X 38    36 0.9473684               F    SEX #> 5  B: Placebo 33    25 0.7575758               M    SEX #> 6   A: Drug X 31    23 0.7419355               M    SEX #> 7  B: Placebo 24    13 0.5416667             low BMRKR2 #> 8   A: Drug X 26    21 0.8076923             low BMRKR2 #> 9  B: Placebo 47    30 0.6382979      low/medium BMRKR2 #> 10  A: Drug X 52    44 0.8461538      low/medium BMRKR2 #> 11 B: Placebo 73    50 0.6849315 low/medium/high BMRKR2 #> 12  A: Drug X 69    59 0.8550725 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $or #>   arm n_tot        or      lcl       ucl conf_level        subgroup    var #> 1       142  2.714000 1.180449  6.239827       0.95    All Patients    ALL #> 2        78 10.800000 2.266958 51.452218       0.95               F    SEX #> 3        64  0.920000 0.296647  2.853223       0.95               M    SEX #> 4        50  3.553846 1.004737 12.570277       0.95             low BMRKR2 #> 5        99  3.116667 1.193409  8.139385       0.95      low/medium BMRKR2 #> 6       142  2.714000 1.180449  6.239827       0.95 low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                          Sex analysis #> 3                          Sex analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #>   # Table with default columns basic_table() %>%   tabulate_rsp_subgroups(df) #>                                             B: Placebo           A: Drug X                                  #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI     #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                         #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45) #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)  # Table with selected columns basic_table() %>%   tabulate_rsp_subgroups(     df = df,     vars = c(\"n_tot\", \"n\", \"n_rsp\", \"prop\", \"or\", \"ci\")   ) #>                                                    B: Placebo                       A: Drug X                                         #> Baseline Risk Factors          Total n   n    Responders   Response (%)   n    Responders   Response (%)   Odds Ratio      95% CI     #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73       50          68.5%       69       59          85.5%          2.71      (1.18, 6.24)  #> Sex                                                                                                                                   #>   F                              78      40       25          62.5%       38       36          94.7%         10.80      (2.27, 51.45) #>   M                              64      33       25          75.8%       31       23          74.2%          0.92      (0.30, 2.85)  #> Continuous Level Biomarker 2                                                                                                          #>   LOW                            50      24       13          54.2%       26       21          80.8%          3.55      (1.00, 12.57) #>   MEDIUM                         49      23       17          73.9%       26       23          88.5%          2.71      (0.59, 12.39) #>   HIGH                           43      26       20          76.9%       17       15          88.2%          2.25      (0.40, 12.75)  # Table with risk difference column added basic_table() %>%   tabulate_rsp_subgroups(     df,     riskdiff = control_riskdiff(       arm_x = levels(df$prop$arm)[1],       arm_y = levels(df$prop$arm)[2]     )   ) #>                                             B: Placebo           A: Drug X                                                                 #> Baseline Risk Factors          Total n   n    Response (%)   n    Response (%)   Odds Ratio      95% CI       Risk Difference (%) (95% CI) #> —————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> All Patients                     142     73      68.5%       69      85.5%          2.71      (1.18, 6.24)        -17.0 (-30.5 - -3.5)     #> Sex                                                                                                                                        #>   F                              78      40      62.5%       38      94.7%         10.80      (2.27, 51.45)      -32.2 (-48.8 - -15.6)     #>   M                              64      33      75.8%       31      74.2%          0.92      (0.30, 2.85)         1.6 (-19.7 - 22.8)      #> Continuous Level Biomarker 2                                                                                                               #>   LOW                            50      24      54.2%       26      80.8%          3.55      (1.00, 12.57)       -26.6 (-51.6 - -1.6)     #>   MEDIUM                         49      23      73.9%       26      88.5%          2.71      (0.59, 12.39)       -14.5 (-36.3 - 7.2)      #>   HIGH                           43      26      76.9%       17      88.2%          2.25      (0.40, 12.75)       -11.3 (-33.6 - 11.0)"},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert rtable objects to ggplot objects — rtable2gg","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"Given rtables::rtable() object, performs basic conversion ggplot2::ggplot() object built using functions ggplot2 package. table titles /footnotes ignored.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"rtable2gg(tbl, fontsize = 12, colwidths = NULL, lbl_col_padding = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"tbl (VTableTree)rtables table object. fontsize (numeric(1)) font size. colwidths (numeric NULL) vector column widths. element's position colwidths corresponds column tbl position. NULL, column widths calculated according maximum number characters per column. lbl_col_padding (numeric) additional padding use calculating spacing first (label) column second column tbl. colwidths specified, width first column becomes colwidths[1] + lbl_col_padding. Defaults 0.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"ggplot object.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtable2gg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert rtable objects to ggplot objects — rtable2gg","text":"","code":"dta <- data.frame(   ARM     = rep(LETTERS[1:3], rep(6, 3)),   AVISIT  = rep(paste0(\"V\", 1:3), 6),   AVAL    = c(9:1, rep(NA, 9)) )  lyt <- basic_table() %>%   split_cols_by(var = \"ARM\") %>%   split_rows_by(var = \"AVISIT\") %>%   analyze_vars(vars = \"AVAL\")  tbl <- build_table(lyt, df = dta)  rtable2gg(tbl)   rtable2gg(tbl, fontsize = 15, colwidths = c(2, 1, 1, 1))"},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions for accessing information from rtables — rtables_access","title":"Helper functions for accessing information from rtables — rtables_access","text":"couple functions help accessing data rtables objects. Currently work occurrence tables, defined count first element fraction second element cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"h_row_first_values(table_row, col_names = NULL, col_indices = NULL)  h_row_counts(table_row, col_names = NULL, col_indices = NULL)  h_row_fractions(table_row, col_names = NULL, col_indices = NULL)  h_col_counts(table, col_names = NULL, col_indices = NULL)  h_content_first_row(table)  is_leaf_table(table)  check_names_indices(table_row, col_names = NULL, col_indices = NULL)"},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions for accessing information from rtables — rtables_access","text":"table_row (TableRow) analysis row occurrence table. col_names (character) names columns extract . col_indices (integer) indices columns extract . col_names provided, inferred names table_row. Note currently works well single column split. table (VTableNodeInfo) occurrence table row.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values() returns vector numeric values. h_row_counts() returns vector numeric values. h_row_fractions() returns vector proportions. h_col_counts() returns vector column counts. h_content_first_row() returns row rtables table. is_leaf_table() returns logical value indicating whether current table leaf. check_names_indices returns column indices.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Helper functions for accessing information from rtables — rtables_access","text":"h_row_first_values(): Helper function extract first values content cell specified columns TableRow. Defaults columns. h_row_counts(): Helper function extracts row values checks convertible integers (integerish values). h_row_fractions(): Helper function extract fractions specified columns TableRow. specifically extracts second values content cell checks fraction. h_col_counts(): Helper function extract column counts specified columns table. h_content_first_row(): Helper function get first row content table current table. is_leaf_table(): Helper function says whether current table leaf tree. check_names_indices(): Internal helper function tests standard inputs column indices.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/rtables_access.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions for accessing information from rtables — rtables_access","text":"","code":"tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"RACE\") %>%   analyze(\"AGE\", function(x) {     list(       \"mean (sd)\" = rcell(c(mean(x), sd(x)), format = \"xx.x (xx.x)\"),       \"n\" = length(x),       \"frac\" = rcell(c(0.1, 0.1), format = \"xx (xx)\")     )   }) %>%   build_table(tern_ex_adsl) %>%   prune_table() tree_row_elem <- collect_leaves(tbl[2, ])[[1]] result <- max(h_row_first_values(tree_row_elem)) result #> [1] 35.31214  # Row counts (integer values) # h_row_counts(tree_row_elem) # Fails because there are no integers # Using values with integers tree_row_elem <- collect_leaves(tbl[3, ])[[1]] result <- h_row_counts(tree_row_elem) # result  # Row fractions tree_row_elem <- collect_leaves(tbl[4, ])[[1]] h_row_fractions(tree_row_elem) #>      A: Drug X     B: Placebo C: Combination  #>            0.1            0.1            0.1"},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":null,"dir":"Reference","previous_headings":"","what":"Bland-Altman analysis — s_bland_altman","title":"Bland-Altman analysis — s_bland_altman","text":"Statistics function uses Bland-Altman method assess agreement two numerical vectors calculates variety statistics.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"s_bland_altman(x, y, conf_level = 0.95)"},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Bland-Altman analysis — s_bland_altman","text":"x (numeric) vector numbers want analyze. y (numeric) vector numbers want analyze, compared x. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Bland-Altman analysis — s_bland_altman","text":"named list following elements: df difference_mean ci_mean difference_sd difference_se upper_agreement_limit lower_agreement_limit agreement_limit_se upper_agreement_limit_ci lower_agreement_limit_ci t_value n","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_bland_altman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Bland-Altman analysis — s_bland_altman","text":"","code":"x <- seq(1, 60, 5) y <- seq(5, 50, 4)  s_bland_altman(x, y, conf_level = 0.9) #> $df #>    average difference #> 1      3.0         -4 #> 2      7.5         -3 #> 3     12.0         -2 #> 4     16.5         -1 #> 5     21.0          0 #> 6     25.5          1 #> 7     30.0          2 #> 8     34.5          3 #> 9     39.0          4 #> 10    43.5          5 #> 11    48.0          6 #> 12    52.5          7 #>  #> $difference_mean #> [1] 1.5 #>  #> $ci_mean #> [1] -0.3692162  3.3692162 #>  #> $difference_sd #> [1] 3.605551 #>  #> $difference_se #> [1] 1.040833 #>  #> $upper_agreement_limit #> [1] 7.430604 #>  #> $lower_agreement_limit #> [1] -4.430604 #>  #> $agreement_limit_se #> [1] 1.802776 #>  #> $upper_agreement_limit_ci #> [1]  4.193027 10.668181 #>  #> $lower_agreement_limit_ci #> [1] -7.668181 -1.193027 #>  #> $t_value #> [1] 1.795885 #>  #> $n #> [1] 12 #>"},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate Cox model - summarized results — s_cox_multivariate","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"Analyses based multivariate Cox model usually performed Controlled Substance Reporting regulatory documents serve exploratory purposes (e.g., publication). practice, model usually includes main effects (without interaction terms). produces hazard ratio estimates covariates included model. analysis follows principles (e.g., stratified vs. unstratified analysis tie handling) usual Cox model analysis. Since usually pre-specified hypothesis testing analysis, p.values need interpreted caution. (Statistical Analysis Clinical Trials Data R, NEST's bookdown)","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"s_cox_multivariate(   formula,   data,   conf_level = 0.95,   pval_method = c(\"wald\", \"likelihood\"),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"formula (formula) formula corresponding investigated survival::Surv() survival model including covariates. data (data.frame) data frame includes variable formula covariates. conf_level (proportion) confidence level hazard ratio interval estimations. Default 0.95. pval_method (string) method used estimation p-values, one \"wald\" (default) \"likelihood\". ... optional parameters passed survival::coxph(). Can include ties, character string specifying method tie handling, one exact (default), efron, breslow.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"list elements mod, msum, aov, coef_inter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"output limited single effect terms. Work ongoing estimation interaction terms scope defined  Global Data Standards Repository (GDS_Standard_TLG_Specs_Tables_2.doc).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/s_cox_multivariate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate Cox model - summarized results — s_cox_multivariate","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte adtte_f <- subset(adtte, PARAMCD == \"OS\") # _f: filtered adtte_f <- filter(   adtte_f,   PARAMCD == \"OS\" &     SEX %in% c(\"F\", \"M\") &     RACE %in% c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"WHITE\") ) adtte_f$SEX <- droplevels(adtte_f$SEX) adtte_f$RACE <- droplevels(adtte_f$RACE)"},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert strings to NA — sas_na","title":"Convert strings to NA — sas_na","text":"SAS imports missing data empty strings strings whitespaces . helper function can used convert values NAs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(x, empty = TRUE, whitespaces = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert strings to NA — sas_na","text":"x (factor character) values missing values substituted. empty (flag) TRUE, empty strings get replaced NA. whitespaces (flag) TRUE, strings made whitespaces get replaced NA.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert strings to NA — sas_na","text":"x \"\" /whitespace-values substituted NA, depending values empty whitespaces.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/sas_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert strings to NA — sas_na","text":"","code":"sas_na(c(\"1\", \"\", \" \", \"   \", \"b\")) #> [1] \"1\" NA  NA  NA  \"b\" sas_na(factor(c(\"\", \" \", \"b\"))) #> [1] <NA> <NA> b    #> Levels: b  is.na(sas_na(c(\"1\", \"\", \" \", \"   \", \"b\"))) #> [1] FALSE  TRUE  TRUE  TRUE FALSE"},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":null,"dir":"Reference","previous_headings":"","what":"Occurrence table sorting — score_occurrences","title":"Occurrence table sorting — score_occurrences","text":"Functions score occurrence table subtables rows can used sorting occurrence tables.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Occurrence table sorting — score_occurrences","text":"","code":"score_occurrences(table_row)  score_occurrences_cols(...)  score_occurrences_subtable(...)  score_occurrences_cont_cols(...)"},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Occurrence table sorting — score_occurrences","text":"table_row (TableRow) analysis row occurrence table. ... arguments row column access, see rtables_access: either col_names (character) including names columns used, alternatively col_indices (integer) giving indices directly instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences() returns sum counts across columns table row. score_occurrences_cols() returns function sums counts across specified columns table row. score_occurrences_subtable() returns function sums counts subtable across specified columns. score_occurrences_cont_cols() returns function sums counts first content row specified columns.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Occurrence table sorting — score_occurrences","text":"score_occurrences(): Scoring function sums counts across columns. fail anything else counts used. score_occurrences_cols(): Scoring functions can produced constructor include specific columns scoring. See h_row_counts() information. score_occurrences_subtable(): Scoring functions produced constructor can used subtables: sum specified column counts subtable. useful available content row summing counts. score_occurrences_cont_cols(): Produces score function sorting table summing first content row specified columns. Note extending rtables::cont_n_onecol() rtables::cont_n_allcols().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/score_occurrences.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Occurrence table sorting — score_occurrences","text":"","code":"lyt <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(     vars = \"USUBJID\",     .stats = c(\"unique\"),     .labels = c(\"Total number of patients with at least one event\")   ) %>%   split_rows_by(\"AEBODSYS\", child_labels = \"visible\", nested = FALSE) %>%   summarize_num_patients(     var = \"USUBJID\",     .stats = c(\"unique\", \"nonunique\"),     .labels = c(       \"Total number of patients with at least one event\",       \"Total number of events\"     )   ) %>%   count_occurrences(vars = \"AEDECOD\")  tbl <- build_table(lyt, tern_ex_adae, alt_counts_df = tern_ex_adsl) %>%   prune_table()  tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_occurrences)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_cols_a_and_b <- score_occurrences_cols(col_names = c(\"A: Drug X\", \"B: Placebo\"))  # Note that this here just sorts the AEDECOD inside the AEBODSYS. The AEBODSYS are not sorted. # That would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\", \"*\", \"AEDECOD\"), scorefun = score_cols_a_and_b)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)    score_subtable_all <- score_occurrences_subtable(col_names = names(tbl))  # Note that this code just sorts the AEBODSYS, not the AEDECOD within AEBODSYS. That # would require a second pass of `sort_at_path`. tbl_sorted <- tbl %>%   sort_at_path(path = c(\"AEBODSYS\"), scorefun = score_subtable_all, decreasing = FALSE)  tbl_sorted #>                                                      A: Drug X    B: Placebo   C: Combination #>                                                        (N=69)       (N=73)         (N=58)     #> ————————————————————————————————————————————————————————————————————————————————————————————— #> Total number of patients with at least one event     59 (85.5%)   57 (78.1%)     48 (82.8%)   #> cl C.2                                                                                        #>   Total number of patients with at least one event   20 (29.0%)   14 (19.2%)     10 (17.2%)   #>   Total number of events                                 21           15             14       #>     dcd C.2.1.2.1                                    20 (29.0%)   14 (19.2%)     10 (17.2%)   #> cl C.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   13 (17.8%)     18 (31.0%)   #>   Total number of events                                 17           15             19       #>     dcd C.1.1.1.3                                    15 (21.7%)   13 (17.8%)     18 (31.0%)   #> cl B.1                                                                                        #>   Total number of patients with at least one event   15 (21.7%)   19 (26.0%)     15 (25.9%)   #>   Total number of events                                 19           19             18       #>     dcd B.1.1.1.1                                    15 (21.7%)   19 (26.0%)     15 (25.9%)   #> cl D.2                                                                                        #>   Total number of patients with at least one event   21 (30.4%)   20 (27.4%)     12 (20.7%)   #>   Total number of events                                 27           22             15       #>     dcd D.2.1.5.3                                    21 (30.4%)   20 (27.4%)     12 (20.7%)   #> cl D.1                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     20 (34.5%)   #>   Total number of events                                 39           35             28       #>     dcd D.1.1.1.1                                    17 (24.6%)   18 (24.7%)     7 (12.1%)    #>     dcd D.1.1.4.2                                    16 (23.2%)   13 (17.8%)     16 (27.6%)   #> cl B.2                                                                                        #>   Total number of patients with at least one event   29 (42.0%)   27 (37.0%)     24 (41.4%)   #>   Total number of events                                 40           38             33       #>     dcd B.2.1.2.1                                    17 (24.6%)   16 (21.9%)     13 (22.4%)   #>     dcd B.2.2.3.1                                    17 (24.6%)   15 (20.5%)     16 (27.6%)   #> cl A.1                                                                                        #>   Total number of patients with at least one event   31 (44.9%)   24 (32.9%)     27 (46.6%)   #>   Total number of events                                 39           33             35       #>     dcd A.1.1.1.1                                    17 (24.6%)   17 (23.3%)     14 (24.1%)   #>     dcd A.1.1.1.2                                    17 (24.6%)   14 (19.2%)     17 (29.3%)"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"split_cols_by_groups(lyt, var, groups_list = NULL, ref_group = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split columns by groups of levels — split_cols_by_groups","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. groups_list (named list character) specifies new group levels via names levels belong character vectors elements list. ref_group (data.frame vector) data corresponding reference group. ... additional arguments rtables::split_cols_by() order. instance, control formats (format), add joint column groups (incl_all).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split columns by groups of levels — split_cols_by_groups","text":"layout object suitable passing layouting functions. Adding function rtable layout add column split including given groups table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/split_cols_by_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split columns by groups of levels — split_cols_by_groups","text":"","code":"# 1 - Basic use  # Without group combination `split_cols_by_groups` is # equivalent to [rtables::split_cols_by()]. basic_table() %>%   split_cols_by_groups(\"ARM\") %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X   B: Placebo   C: Combination #>         (N=121)     (N=106)        (N=129)     #> —————————————————————————————————————————————— #> Mean     34.91       33.02          34.57       # Add a reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X   B: Placebo   C: Combination #>              (N=121)     (N=106)        (N=129)     #> ——————————————————————————————————————————————————— #> Diff Mean     1.89                        1.55       # 2 - Adding group specification  # Manual preparation of the groups. groups <- list(   \"Arms A+B\" = c(\"A: Drug X\", \"B: Placebo\"),   \"Arms A+C\" = c(\"A: Drug X\", \"C: Combination\") )  # Use of split_cols_by_groups without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        Arms A+B   Arms A+C #>        (N=227)    (N=250)  #> —————————————————————————— #> Mean    34.03      34.73    # Including differentiated output in the reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups, ref_group = \"Arms A+B\") %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff. of Averages\" = rcell(NULL))       } else {         in_rows(\"Diff. of Averages\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>                     Arms A+B   Arms A+C #> ——————————————————————————————————————— #> Diff. of Averages                0.71    # 3 - Binary list dividing factor levels into reference and treatment  # `combine_groups` defines reference and treatment. groups <- combine_groups(   fct = DM$ARM,   ref = c(\"A: Drug X\", \"B: Placebo\") ) groups #> $`A: Drug X/B: Placebo` #> [1] \"A: Drug X\"  \"B: Placebo\" #>  #> $`C: Combination` #> [1] \"C: Combination\" #>   # Use group definition without reference column. basic_table() %>%   split_cols_by_groups(\"ARM\", groups_list = groups) %>%   add_colcounts() %>%   analyze(\"AGE\") %>%   build_table(DM) #>        A: Drug X/B: Placebo   C: Combination #>              (N=227)             (N=129)     #> ———————————————————————————————————————————— #> Mean          34.03               34.57       # Use group definition with reference column (first item of groups). basic_table() %>%   split_cols_by_groups(\"ARM\", groups, ref_group = names(groups)[1]) %>%   add_colcounts() %>%   analyze(     \"AGE\",     afun = function(x, .ref_group, .in_ref_col) {       if (.in_ref_col) {         in_rows(\"Diff Mean\" = rcell(NULL))       } else {         in_rows(\"Diff Mean\" = rcell(mean(x) - mean(.ref_group), format = \"xx.xx\"))       }     }   ) %>%   build_table(DM) #>             A: Drug X/B: Placebo   C: Combination #>                   (N=227)             (N=129)     #> ————————————————————————————————————————————————— #> Diff Mean                               0.54"},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":null,"dir":"Reference","previous_headings":"","what":"Split text according to available text width — split_text_grob","title":"Split text according to available text width — split_text_grob","text":"Dynamically wrap text.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split text according to available text width — split_text_grob","text":"","code":"split_text_grob(   text,   x = grid::unit(0.5, \"npc\"),   y = grid::unit(0.5, \"npc\"),   width = grid::unit(1, \"npc\"),   just = \"centre\",   hjust = NULL,   vjust = NULL,   default.units = \"npc\",   name = NULL,   gp = grid::gpar(),   vp = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split text according to available text width — split_text_grob","text":"text (string) text wrap. x numeric vector unit object specifying x-values. y numeric vector unit object specifying y-values. width (grid::unit) unit object specifying maximum width text. just justification text     relative (x, y) location.  two values, first     value specifies horizontal justification second value specifies     vertical justification.  Possible string values : \"left\",     \"right\", \"centre\", \"center\", \"bottom\",     \"top\".  numeric values, 0 means left (bottom) alignment     1 means right (top) alignment. hjust numeric vector specifying horizontal justification.     specified, overrides just setting. vjust numeric vector specifying vertical justification.     specified, overrides just setting. default.units string indicating default units use     x y     given numeric vectors. name character identifier. gp object class \"gpar\", typically output     call function gpar.  basically     list graphical parameter settings. vp Grid viewport object (NULL).","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split text according to available text width — split_text_grob","text":"text grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/split_text_grob.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split text according to available text width — split_text_grob","text":"code taken R Graphics Paul Murell, 2nd edition","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Stack multiple grobs — stack_grobs","title":"Stack multiple grobs — stack_grobs","text":"Stack grobs new grob 1 column multiple rows layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stack multiple grobs — stack_grobs","text":"","code":"stack_grobs(   ...,   grobs = list(...),   padding = grid::unit(2, \"line\"),   vp = NULL,   gp = NULL,   name = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stack multiple grobs — stack_grobs","text":"... grobs. grobs (list grob) list grobs. padding (grid::unit) unit length 1, space grob. vp (viewport NULL) viewport() object (NULL). gp (gpar) gpar() object. name (string) character identifier grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stack multiple grobs — stack_grobs","text":"grob.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stack_grobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stack multiple grobs — stack_grobs","text":"","code":"library(grid)  g1 <- circleGrob(gp = gpar(col = \"blue\")) g2 <- circleGrob(gp = gpar(col = \"red\")) g3 <- textGrob(\"TEST TEXT\") grid.newpage() grid.draw(stack_grobs(g1, g2, g3))  showViewport()   grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vp1 <- viewport(layout.pos.row = 1, layout.pos.col = 2) grid.draw(stack_grobs(g1, g2, g3, vp = vp1, name = \"test\"))  showViewport()  grid.ls(grobs = TRUE, viewports = TRUE, print = FALSE)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for mean — stat_mean_ci","title":"Confidence interval for mean — stat_mean_ci","text":"Convenient function calculating mean confidence interval. calculates arithmetic well geometric mean. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(   x,   conf_level = 0.95,   na.rm = TRUE,   n_min = 2,   gg_helper = TRUE,   geom_mean = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for mean — stat_mean_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate confidence interval mean. gg_helper (flag) whether output aligned use ggplots. geom_mean (flag) whether geometric mean calculated.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for mean — stat_mean_ci","text":"named vector values mean_ci_lwr mean_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for mean — stat_mean_ci","text":"","code":"stat_mean_ci(sample(10), gg_helper = FALSE) #> mean_ci_lwr mean_ci_upr  #>    3.334149    7.665851   p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point()  p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5),   geom = \"errorbar\" )   p + ggplot2::stat_summary(   fun.data = stat_mean_ci,   fun.args = list(conf_level = 0.5, geom_mean = TRUE),   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":null,"dir":"Reference","previous_headings":"","what":"p-Value of the mean — stat_mean_pval","title":"p-Value of the mean — stat_mean_pval","text":"Convenient function calculating two-sided p-value mean.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(x, na.rm = TRUE, n_min = 2, test_mean = 0)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"p-Value of the mean — stat_mean_pval","text":"x (numeric) vector numbers want analyze. na.rm (flag) whether NA values removed x prior analysis. n_min (numeric(1)) minimum number non-missing x estimate p-value mean. test_mean (numeric(1)) mean value test null hypothesis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"p-Value of the mean — stat_mean_pval","text":"p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_mean_pval.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"p-Value of the mean — stat_mean_pval","text":"","code":"stat_mean_pval(sample(10)) #>     p_value  #> 0.000278196   stat_mean_pval(rnorm(10), test_mean = 0.5) #>    p_value  #> 0.04235675"},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence interval for median — stat_median_ci","title":"Confidence interval for median — stat_median_ci","text":"Convenient function calculating median confidence interval. can used ggplot helper function plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(x, conf_level = 0.95, na.rm = TRUE, gg_helper = TRUE)"},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence interval for median — stat_median_ci","text":"x (numeric) vector numbers want analyze. conf_level (proportion) confidence level interval. na.rm (flag) whether NA values removed x prior analysis. gg_helper (flag) whether output aligned use ggplots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence interval for median — stat_median_ci","text":"named vector values median_ci_lwr median_ci_upr.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Confidence interval for median — stat_median_ci","text":"function adapted DescTools/versions/0.99.35/source","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_median_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence interval for median — stat_median_ci","text":"","code":"stat_median_ci(sample(10), gg_helper = FALSE) #> median_ci_lwr median_ci_upr  #>             2             9  #> attr(,\"conf_level\") #> [1] 0.9785156  p <- ggplot2::ggplot(mtcars, ggplot2::aes(cyl, mpg)) +   ggplot2::geom_point() p + ggplot2::stat_summary(   fun.data = stat_median_ci,   geom = \"errorbar\" )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Proportion difference and confidence interval — stat_propdiff_ci","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"Function calculating proportion (risk) difference confidence interval arm X (reference group) arm Y. Risk difference calculated subtracting cumulative incidence arm Y cumulative incidence arm X.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x,   y,   N_x,   N_y,   list_names = NULL,   conf_level = 0.95,   pct = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"x (list integer) list number occurrences arm X (reference group). y (list integer) list number occurrences arm Y. Must equal length x. N_x (numeric(1)) total number records arm X. N_y (numeric(1)) total number records arm Y. list_names (character) names variable/level corresponding pair proportions x y. Must equal length x y. conf_level (proportion) confidence level interval. pct (flag) whether output returned percentages. Defaults TRUE.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"List proportion differences CIs corresponding pair number occurrences x y. list element consists 3 statistics: proportion difference, CI lower bound, CI upper bound.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/stat_propdiff_ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Proportion difference and confidence interval — stat_propdiff_ci","text":"","code":"stat_propdiff_ci(   x = list(0.375), y = list(0.01), N_x = 5, N_y = 5, list_names = \"x\", conf_level = 0.9 ) #> $x #> [1]   7.30000 -12.35184  26.95184 #>   stat_propdiff_ci(   x = list(0.5, 0.75, 1), y = list(0.25, 0.05, 0.5), N_x = 10, N_y = 20, pct = FALSE ) #> [[1]] #> [1]  0.0375000 -0.1060891  0.1810891 #>  #> [[2]] #> [1]  0.07250000 -0.09220915  0.23720915 #>  #> [[3]] #> [1]  0.0750000 -0.1231285  0.2731285 #>"},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"function wraps estimation stratified percentiles assume approximation large numbers. necessary case proportions strata unequal.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_normal_quantile(vars, weights, conf_level)"},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"vars (character) variable names primary analysis variable iterated . weights (numeric NULL) weights level strata. NULL, estimated using iterative algorithm proposed Yan2010-jt;textualtern minimizes weighted squared length confidence interval. conf_level (proportion) confidence level interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"Stratified quantile.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/strata_normal_quantile.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of stratified quantiles — strata_normal_quantile","text":"","code":"strata_data <- table(data.frame(   \"f1\" = sample(c(TRUE, FALSE), 100, TRUE),   \"f2\" = sample(c(\"x\", \"y\", \"z\"), 100, TRUE),   stringsAsFactors = TRUE )) ns <- colSums(strata_data) ests <- strata_data[\"TRUE\", ] / ns vars <- ests * (1 - ests) / ns weights <- rep(1 / length(ns), length(ns))  strata_normal_quantile(vars, weights, 0.95) #> [1] 1.14181"},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":null,"dir":"Reference","previous_headings":"","what":"Indicate study arm variable in formula — study_arm","title":"Indicate study arm variable in formula — study_arm","text":"use study_arm indicate study arm variable tern formulas.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Indicate study arm variable in formula — study_arm","text":"","code":"study_arm(x)"},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Indicate study arm variable in formula — study_arm","text":"x arm information","code":""},{"path":"https://insightsengineering.github.io/tern/reference/study_arm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Indicate study arm variable in formula — study_arm","text":"x","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"analyze function summarize_ancova() creates layout element summarize ANCOVA results. function can used analyze multiple endpoints /multiple timepoints within response variable(s) specified vars. Additional variables analysis, namely arm (grouping) variable covariate variables, can defined via variables argument. See details specify variables. interaction term can implemented model needed. interaction variable interact arm variable specified via interaction_term parameter, specific value interaction_term extract ANCOVA results via interaction_y parameter.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"summarize_ancova(   lyt,   vars,   variables,   conf_level,   interaction_y = FALSE,   interaction_item = NULL,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )  a_ancova(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   conf_level,   interaction_y = FALSE,   interaction_item = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". conf_level (proportion) confidence level interval. interaction_y (string flag) selected item inside interaction_item variable used select specific ANCOVA results. interaction needed, default option FALSE. interaction_item (string NULL) name variable interactions arm. interaction needed, default option NULL. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'lsmean', 'lsmean_diff', 'lsmean_diff_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) data set includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_ancova() table layout. s_ancova() returns named list 5 statistics: n: Count complete sample size group. lsmean: Estimated marginal means group. lsmean_diff: Difference estimated marginal means comparison reference group. working reference group, empty. lsmean_diff_ci: Confidence level difference estimated marginal means comparison reference group. pval: p-value (adjusted multiple comparisons). a_ancova() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"summarize_ancova(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_ancova(): Statistics function produces named list results investigated linear model. a_ancova(): Formatted analysis function used afun summarize_ancova().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_ancova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize analysis of covariance (ANCOVA) results — summarize_ancova","text":"","code":"basic_table() %>%   split_cols_by(\"Species\", ref_group = \"setosa\") %>%   add_colcounts() %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = NULL),     table_names = \"unadj\",     conf_level = 0.95, var_labels = \"Unadjusted comparison\",     .labels = c(lsmean = \"Mean\", lsmean_diff = \"Difference in Means\")   ) %>%   summarize_ancova(     vars = \"Petal.Length\",     variables = list(arm = \"Species\", covariates = c(\"Sepal.Length\", \"Sepal.Width\")),     table_names = \"adj\",     conf_level = 0.95, var_labels = \"Adjusted comparison (covariates: Sepal.Length and Sepal.Width)\"   ) %>%   build_table(iris) #>                                                                  setosa    versicolor     virginica   #>                                                                  (N=50)      (N=50)         (N=50)    #> ————————————————————————————————————————————————————————————————————————————————————————————————————— #> Unadjusted comparison                                                                                 #>   n                                                                50          50             50      #>   Mean                                                            1.46        4.26           5.55     #>   Difference in Means                                                         2.80           4.09     #>     95% CI                                                                (2.63, 2.97)   (3.92, 4.26) #>     p-value                                                                 <0.0001        <0.0001    #> Adjusted comparison (covariates: Sepal.Length and Sepal.Width)                                        #>   n                                                                50          50             50      #>   Adjusted Mean                                                   2.02        4.19           5.07     #>   Difference in Adjusted Means                                                2.17           3.05     #>     95% CI                                                                (1.96, 2.38)   (2.81, 3.29) #>     p-value                                                                 <0.0001        <0.0001"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize change from baseline values or absolute baseline values — summarize_change","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"analyze function summarize_change() creates layout element summarize change baseline absolute baseline values. primary analysis variable vars indicates numerical change baseline results. Required secondary analysis variables value baseline_flag can supplied function via variables argument. value element name analysis value variable, baseline_flag element name flag variable indicates whether records contain baseline values. Depending baseline flag given, either absolute baseline values (baseline) change baseline values (post-baseline) summarized.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"summarize_change(   lyt,   vars,   variables,   na_str = default_na_str(),   nested = TRUE,   ...,   table_names = vars,   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_change_from_baseline(df, .var, variables, na.rm = TRUE, ...)  a_change_from_baseline(df, .var, variables, na.rm = TRUE, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'sum', 'mean', 'sd', 'se', 'mean_sd', 'mean_se', 'mean_ci', 'mean_sei', 'mean_sdi', 'mean_pval', 'median', 'mad', 'median_ci', 'quantiles', 'iqr', 'range', 'min', 'max', 'median_range', 'cv', 'geom_mean', 'geom_mean_ci', 'geom_cv' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. na.rm (flag) whether NA values removed x prior analysis.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_change_from_baseline() table layout. s_change_from_baseline() returns values returned s_summary.numeric(). a_change_from_baseline() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"summarize_change(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_change_from_baseline(): Statistics function summarizes baseline post-baseline visits. a_change_from_baseline(): Formatted analysis function used afun summarize_change().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"used split visits layout, data subset contains either baseline post-baseline data. data df must either baseline post-baseline visits. Otherwise error thrown.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_change.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize change from baseline values or absolute baseline values — summarize_change","text":"","code":"library(dplyr)  ## Fabricate dataset dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)) ) %>%   mutate(ABLFLL = AVISIT == \"V1\") %>%   group_by(USUBJID) %>%   mutate(     BLVAL = AVAL[ABLFLL],     CHG = AVAL - BLVAL   ) %>%   ungroup()  results <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   summarize_change(\"CHG\", variables = list(value = \"AVAL\", baseline_flag = \"ABLFLL\")) %>%   build_table(dta_test)  results #>                     A                 B               C     #> ——————————————————————————————————————————————————————————— #> V1                                                          #>   n                 2                 1               0     #>   Mean (SD)    7.50 (2.12)    3.00 (<Missing>)    <Missing> #>   Median          7.50              3.00          <Missing> #>   Min - Max    6.00 - 9.00       3.00 - 3.00      <Missing> #> V2                                                          #>   n                 2                 1               0     #>   Mean (SD)   -1.00 (0.00)    -1.00 (<Missing>)   <Missing> #>   Median          -1.00             -1.00         <Missing> #>   Min - Max   -1.00 - -1.00     -1.00 - -1.00     <Missing> #> V3                                                          #>   n                 2                 1               0     #>   Mean (SD)   -2.00 (0.00)    -2.00 (<Missing>)   <Missing> #>   Median          -2.00             -2.00         <Missing> #>   Min - Max   -2.00 - -2.00     -2.00 - -2.00     <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize variables in columns — summarize_colvars","title":"Summarize variables in columns — summarize_colvars","text":"analyze function summarize_colvars() uses statistics function s_summary() analyze variables arranged columns. variables analyze specified table layout via column splits (see rtables::split_cols_by() rtables::split_cols_by_multivar()) prior using summarize_colvars(). function minimal wrapper rtables::analyze_colvars(), function typically used apply different analysis methods rows column variable. use analysis methods column labels, please refer analyze_vars_in_cols() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize variables in columns — summarize_colvars","text":"","code":"summarize_colvars(   lyt,   ...,   na_str = default_na_str(),   .stats = c(\"n\", \"mean_sd\", \"median\", \"range\", \"count_fraction\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize variables in columns — summarize_colvars","text":"lyt (PreDataTableLayouts) layout analyses added . ... arguments passed s_summary(). na_str (string) string used replace NA empty values output. .stats (character) statistics select table. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named vector integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize variables in columns — summarize_colvars","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout summarize given variables, arrange output columns, add table layout.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/summarize_colvars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize variables in columns — summarize_colvars","text":"","code":"dta_test <- data.frame(   USUBJID = rep(1:6, each = 3),   PARAMCD = rep(\"lab\", 6 * 3),   AVISIT = rep(paste0(\"V\", 1:3), 6),   ARM = rep(LETTERS[1:3], rep(6, 3)),   AVAL = c(9:1, rep(NA, 9)),   CHG = c(1:9, rep(NA, 9)) )  ## Default output within a `rtables` pipeline. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars() %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>  ## Selection of statistics, formats and labels also work. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(     .stats = c(\"n\", \"mean_sd\"),     .formats = c(\"mean_sd\" = \"xx.x, xx.x\"),     .labels = c(n = \"n\", mean_sd = \"Mean, SD\")   ) %>%   build_table(dta_test) #>                       A                           B                            C           #>                AVAL       CHG           AVAL             CHG           AVAL         CHG    #> —————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   7.5, 2.1   2.5, 2.1   3.0, <Missing>   7.0, <Missing>   <Missing>   <Missing> #> V2                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   6.5, 2.1   3.5, 2.1   2.0, <Missing>   8.0, <Missing>   <Missing>   <Missing> #> V3                                                                                         #>   n             2          2             1                1              0           0     #>   Mean, SD   5.5, 2.1   4.5, 2.1   1.0, <Missing>   9.0, <Missing>   <Missing>   <Missing>  ## Use arguments interpreted by `s_summary`. basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"AVISIT\") %>%   split_cols_by_multivar(vars = c(\"AVAL\", \"CHG\")) %>%   summarize_colvars(na.rm = FALSE) %>%   build_table(dta_test) #>                         A                             B                             C           #>                 AVAL         CHG           AVAL               CHG           AVAL         CHG    #> ——————————————————————————————————————————————————————————————————————————————————————————————— #> V1                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   7.5 (2.1)   2.5 (2.1)   3.0 (<Missing>)   7.0 (<Missing>)   <Missing>   <Missing> #>   Median         7.5         2.5            3.0               7.0         <Missing>   <Missing> #>   Min - Max   6.0 - 9.0   1.0 - 4.0      3.0 - 3.0         7.0 - 7.0      <Missing>   <Missing> #> V2                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   6.5 (2.1)   3.5 (2.1)   2.0 (<Missing>)   8.0 (<Missing>)   <Missing>   <Missing> #>   Median         6.5         3.5            2.0               8.0         <Missing>   <Missing> #>   Min - Max   5.0 - 8.0   2.0 - 5.0      2.0 - 2.0         8.0 - 8.0      <Missing>   <Missing> #> V3                                                                                              #>   n               2           2              1                 1              0           0     #>   Mean (SD)   5.5 (2.1)   4.5 (2.1)   1.0 (<Missing>)   9.0 (<Missing>)   <Missing>   <Missing> #>   Median         5.5         4.5            1.0               9.0         <Missing>   <Missing> #>   Min - Max   4.0 - 7.0   3.0 - 6.0      1.0 - 1.0         9.0 - 9.0      <Missing>   <Missing>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_functions.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize functions — summarize_functions","title":"Summarize functions — summarize_functions","text":"functions wrappers rtables::summarize_row_groups(), applying corresponding tern content functions add summary rows given table layout:","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_functions.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize functions — summarize_functions","text":"add_rowcounts() estimate_multinomial_response() (rtables::analyze()) h_tab_one_biomarker() (probably deprecate) logistic_summary_by_flag() summarize_num_patients() summarize_occurrences() summarize_occurrences_by_grade() summarize_patients_events_in_cols() summarize_patients_exposure_in_cols() Additionally, summarize_coxreg() function utilizes rtables::summarize_row_groups() (combination several rtables functions like rtables::analyze_colvars()) output Cox regression summary table.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize Poisson negative binomial regression — summarize_glm_count","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"Summarize results Poisson negative binomial regression. can used analyze count /frequency data using linear model. specifically useful analyzing count data (using Poisson Negative Binomial distribution) result generalized linear model one (e.g. arm) covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"summarize_glm_count(   lyt,   vars,   variables,   distribution,   conf_level,   rate_mean_method = c(\"emmeans\", \"ppmeans\")[1],   weights = stats::weights,   scale = 1,   var_labels,   na_str = default_na_str(),   nested = TRUE,   ...,   show_labels = \"visible\",   table_names = vars,   .stats = get_stats(\"summarize_glm_count\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(n = 0L, rate = 0L, rate_ci = 1L, rate_ratio = 0L, rate_ratio_ci = 1L,     pval = 1L) )  s_glm_count(   df,   .var,   .df_row,   variables,   .ref_group,   .in_ref_col,   distribution,   conf_level,   rate_mean_method,   weights,   scale = 1 )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . variables (named list string) list additional analysis variables, expected elements: arm (string) group variable, covariate adjusted means multiple groups summarized. Specifically, first level arm variable taken reference group. covariates (character) vector can contain single variable names (\"X1\"), /interaction terms indicated \"X1 * X2\". offset (numeric) numeric vector scalar adding offset. distribution (character) character value specifying distribution used regression (Poisson, Quasi-Poisson, negative binomial). conf_level (proportion) confidence level interval. rate_mean_method (character(1)) method used estimate mean odds ratio. Defaults emmeans. see details information. weights (character) character vector specifying weights used averaging predictions. Number weights must equal number levels included covariates. Weights option passed emmeans::emmeans(). scale (numeric(1)) linear scaling factor rate confidence intervals. Defaults 1. var_labels (character) variable labels. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'n', 'rate', 'rate_ci', 'rate_ratio', 'rate_ratio_ci', 'pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .df_row (data.frame) dataset includes variables called .var variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_glm_count() table layout. s_glm_count() returns named list 5 statistics: n: Count complete sample size group. rate: Estimated event rate per follow-time. rate_ci: Confidence level estimated rate per follow-time. rate_ratio: Ratio event rates treatment arm reference arm. rate_ratio_ci: Confidence level rate ratio. pval: p-value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count() uses s_glm_count() calculate statistics table. analysis function uses h_glm_count() estimate GLM stats::glm() Poisson Quasi-Poisson distributions MASS::glm.nb() Negative Binomial distribution. methods assume logarithmic link function. point, rates confidence intervals estimated model using either emmeans::emmeans() rate_mean_method = \"emmeans\" h_ppmeans() rate_mean_method = \"ppmeans\". reference group specified building table split_cols_by(ref_group), rate ratio p-value calculated. Otherwise, use emmeans::contrast() calculate rate ratio p-value reference group. Values always estimated method = \"trt.vs.ctrl\" ref equal first arm value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"summarize_glm_count(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_glm_count(): Statistics function produces named list results investigated Poisson model.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_glm_count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summarize Poisson negative binomial regression — summarize_glm_count","text":"","code":"library(dplyr)  anl <- tern_ex_adtte %>% filter(PARAMCD == \"TNE\") anl$AVAL_f <- as.factor(anl$AVAL)  lyt <- basic_table() %>%   split_cols_by(\"ARM\", ref_group = \"B: Placebo\") %>%   add_colcounts() %>%   analyze_vars(     \"AVAL_f\",     var_labels = \"Number of exacerbations per patient\",     .stats = c(\"count_fraction\"),     .formats = c(\"count_fraction\" = \"xx (xx.xx%)\"),     .labels = c(\"Number of exacerbations per patient\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = NULL),     conf_level = 0.95,     distribution = \"poisson\",     rate_mean_method = \"emmeans\",     var_labels = \"Adjusted (P) exacerbation rate (per year)\",     table_names = \"adjP\",     .stats = c(\"rate\"),     .labels = c(rate = \"Rate\")   ) %>%   summarize_glm_count(     vars = \"AVAL\",     variables = list(arm = \"ARM\", offset = \"lgTMATRSK\", covariates = c(\"REGION1\")),     conf_level = 0.95,     distribution = \"quasipoisson\",     rate_mean_method = \"ppmeans\",     var_labels = \"Adjusted (QP) exacerbation rate (per year)\",     table_names = \"adjQP\",     .stats = c(\"rate\", \"rate_ci\", \"rate_ratio\", \"rate_ratio_ci\", \"pval\"),     .labels = c(       rate = \"Rate\", rate_ci = \"Rate CI\", rate_ratio = \"Rate Ratio\",       rate_ratio_ci = \"Rate Ratio CI\", pval = \"p value\"     )   )  build_table(lyt = lyt, df = anl) #>                                                 A: Drug X          B: Placebo       C: Combination  #>                                                   (N=69)             (N=73)             (N=58)      #> ——————————————————————————————————————————————————————————————————————————————————————————————————— #> Number of exacerbations per patient                                                                 #>   0                                             3 (4.35%)          8 (10.96%)         6 (10.34%)    #>   1                                            11 (15.94%)         9 (12.33%)         6 (10.34%)    #>   2                                            18 (26.09%)        15 (20.55%)         9 (15.52%)    #>   3                                            14 (20.29%)        11 (15.07%)        15 (25.86%)    #>   4                                            10 (14.49%)         9 (12.33%)         9 (15.52%)    #>   5                                             7 (10.14%)         9 (12.33%)         8 (13.79%)    #>   6                                             4 (5.80%)          4 (5.48%)          4 (6.90%)     #>   7                                             2 (2.90%)          8 (10.96%)         0 (0.00%)     #>   10                                            0 (0.00%)          0 (0.00%)          1 (1.72%)     #> Adjusted (P) exacerbation rate (per year)                                                           #>   Rate                                            8.2061             9.1554             7.8551      #> Adjusted (QP) exacerbation rate (per year)                                                          #>   Rate                                            3.1214             3.4860             2.6152      #>     Rate CI                                  (1.7307, 5.6294)   (1.9833, 6.1272)   (1.3661, 5.0065) #>   Rate Ratio                                      0.8954                                0.7502      #>     Rate Ratio CI                            (0.3975, 2.0170)                      (0.3067, 1.8348) #>     p value                                       0.7897                                0.5288"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":null,"dir":"Reference","previous_headings":"","what":"Multivariate logistic regression table — summarize_logistic","title":"Multivariate logistic regression table — summarize_logistic","text":"Layout-creating function summarizes logistic variable regression binary outcome categorical/continuous covariates model statement. covariate category (categorical) specified values (continuous), present degrees freedom, regression parameter estimate standard error (SE) relative reference group category. Report odds ratios covariate category specified values corresponding Wald confidence intervals default allow user specify confidence levels. Report p-value Wald chi-square test null hypothesis covariate effect response model containing specified covariates. Allow option include one two-way interaction present similar output interaction degree freedom.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"summarize_logistic(   lyt,   conf_level,   drop_and_remove_str = \"\",   .indent_mods = NULL )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multivariate logistic regression table — summarize_logistic","text":"lyt (PreDataTableLayouts) layout analyses added . conf_level (proportion) confidence level interval. drop_and_remove_str (string) string dropped removed. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multivariate logistic regression table — summarize_logistic","text":"layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add logistic regression variable summary table layout.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Multivariate logistic regression table — summarize_logistic","text":"formula, variable names need standard data.frame column names without special characters.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_logistic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Multivariate logistic regression table — summarize_logistic","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)  # flagging empty strings with \"_\" df <- df_explicit_na(df, na_level = \"_\") df2 <- df_explicit_na(df2, na_level = \"_\")  result1 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df) result1 #>                                       Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Planned Arm Code                              2                                                                                 0.3004  #>   Reference ARM A, n = 64                                                                                                               #>   ARM B, n = 68                               1                  -1.775             1.144           0.17       (<0.01, 3.23)    0.1209  #>   ARM C, n = 52                               1                  17.192            3626.588       >999.99     (0.00, >999.99)   0.9962  #> Age                                                                                                                                     #>   Age                                         1                  0.170              0.095           1.19       (0.93, 1.51)     0.0746  #> Race                                          2                                                                                 0.7967  #>   Reference ASIAN, n = 110                                                                                                              #>   BLACK OR AFRICAN AMERICAN, n = 40           1                  17.923            4001.705       >999.99     (0.00, >999.99)   0.9964  #>   WHITE, n = 34                               1                  -0.656             0.974           0.52       (0.04, 6.37)     0.5002   result2 <- basic_table() %>%   summarize_logistic(     conf_level = 0.95,     drop_and_remove_str = \"_\"   ) %>%   build_table(df = df2) result2 #>                                         Degrees of Freedom   Parameter Estimate   Standard Error   Odds Ratio     Wald 95% CI     p-value #> ————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Race                                            2                                                                                 0.9361  #>   Reference ASIAN, n = 110                                                                                                                #>   BLACK OR AFRICAN AMERICAN, n = 40             1                  18.150            3944.701       >999.99     (0.00, >999.99)   0.9963  #>   WHITE, n = 34                                 1                  -0.373             1.026           0.69       (0.05, 9.68)     0.7164  #> Planned Arm Code                                2                                                                                 0.2539  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                 -11.527             6.962                                       0.0978  #>     Age                                                                                                                                   #>       35                                                                                              0.48       (0.01, 15.48)            #>   ARM C, n = 52                                 1                  16.333           20278.387                                     0.9994  #>     Age                                                                                                                                   #>       35                                                                                            >999.99     (0.00, >999.99)           #> Age                                                                                                                                       #>   Age                                           1                  -0.039             0.151                                       0.7981  #>     Planned Arm Code                                                                                                                      #>       ARM A                                                                                           0.96       (0.65, 1.42)             #>       ARM B                                                                                           1.31       (0.92, 1.86)             #>       ARM C                                                                                           0.99      (0.00, >999.99)           #> Interaction of Planned Arm Code * Age           2                                                                                 0.3276  #>   Reference ARM A, n = 64                                                                                                                 #>   ARM B, n = 68                                 1                  0.308              0.206                                       0.1352  #>   ARM C, n = 52                                 1                  0.029             548.592                                      1.0000"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients — summarize_num_patients","title":"Count number of patients — summarize_num_patients","text":"analyze function analyze_num_patients() creates layout element count total numbers unique non-unique patients. primary analysis variable vars used uniquely identify patients. count_by variable can used identify non-unique patients number patients unique combination values vars count_by returned instead nonunique statistic. required variable can used specify variable required non-missing record included counts. summarize function summarize_num_patients() performs function analyze_num_patients() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients — summarize_num_patients","text":"","code":"analyze_num_patients(   lyt,   vars,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   nested = TRUE,   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   show_labels = c(\"default\", \"visible\", \"hidden\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  summarize_num_patients(   lyt,   var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE,   na_str = default_na_str(),   .stats = NULL,   .formats = NULL,   .labels = c(unique = \"Number of patients with at least one event\", nonunique =     \"Number of events\"),   .indent_mods = 0L,   riskdiff = FALSE,   ... )  s_num_patients(   x,   labelstr,   .N_col,   count_by = NULL,   unique_count_suffix = TRUE )  s_num_patients_content(   df,   labelstr = \"\",   .N_col,   .var,   required = NULL,   count_by = NULL,   unique_count_suffix = TRUE )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients — summarize_num_patients","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . required (character NULL) name variable required non-missing. count_by (character NULL) name variable combined vars counting nonunique records. unique_count_suffix (flag) whether \"(n)\" suffix added unique_count labels. Defaults TRUE. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. .stats (character) statistics select table. Options : 'unique', 'nonunique', 'unique_count' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. riskdiff (flag) whether risk difference column present. set TRUE, add_riskdiff() must used split_fun prior column split table layout, specifying columns compared. See stat_propdiff_ci() details risk difference calculation. ... additional arguments lower level functions. x (character factor) vector patient IDs. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. df (data.frame) data set containing analysis variables. .var, var (string) single variable name passed rtables requested statistics function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. summarize_num_patients() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_num_patients_content() table layout. s_num_patients() returns named list 3 statistics: unique: Vector counts percentages. nonunique: Vector counts. unique_count: Counts. s_num_patients_content() returns values s_num_patients().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count number of patients — summarize_num_patients","text":"general, functions starts analyze* expected work like rtables::analyze(), functions starts summarize* based upon rtables::summarize_row_groups(). latter provides value dividing split row column space, , bound fundamental splits, repeated design every page pagination involved.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients — summarize_num_patients","text":"analyze_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). summarize_num_patients(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::summarize_row_groups(). s_num_patients(): Statistics function counts number unique patients, corresponding percentage taken respect total number patients, number non-unique patients. s_num_patients_content(): Statistics function counts number unique patients column (variable), corresponding percentage taken respect total number patients, number non-unique patients column.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients — summarize_num_patients","text":"opposed summarize_num_patients(), function repeat produced rows.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_num_patients.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients — summarize_num_patients","text":"","code":"df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA, 6, 6, 8, 9)),   ARM = c(\"A\", \"A\", \"A\", \"A\", \"A\", \"B\", \"B\", \"B\", \"B\"),   AGE = c(10, 15, 10, 17, 8, 11, 11, 19, 17),   SEX = c(\"M\", \"M\", \"M\", \"F\", \"F\", \"F\", \"M\", \"F\", \"M\") )  # analyze_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   add_colcounts() %>%   analyze_num_patients(\"USUBJID\", .stats = c(\"unique\")) %>%   build_table(df)  tbl #>                                                  A           B     #>                                                (N=5)       (N=4)   #> —————————————————————————————————————————————————————————————————— #> Number of patients with at least one event   3 (60.0%)   3 (75.0%)  # summarize_num_patients tbl <- basic_table() %>%   split_cols_by(\"ARM\") %>%   split_rows_by(\"SEX\") %>%   summarize_num_patients(\"USUBJID\", .stats = \"unique_count\") %>%   build_table(df)  tbl #>         A   B #> ————————————— #> M (n)   2   2 #> F (n)   1   2  # Use the statistics function to count number of unique and nonunique patients. s_num_patients(x = as.character(c(1, 1, 1, 2, 4, NA)), labelstr = \"\", .N_col = 6L) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 5 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>  s_num_patients(   x = as.character(c(1, 1, 1, 2, 4, NA)),   labelstr = \"\",   .N_col = 6L,   count_by = c(1, 1, 2, 1, 1, 1) ) #> $unique #> [1] 3.0 0.5 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   # Count number of unique and non-unique patients.  df <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = as.character(c(10, 15, 10, 17, 8)) ) s_num_patients_content(df, .N_col = 5, .var = \"USUBJID\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 4 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>   df_by_event <- data.frame(   USUBJID = as.character(c(1, 2, 1, 4, NA)),   EVENT = c(10, 15, 10, 17, 8) ) s_num_patients_content(df_by_event, .N_col = 5, .var = \"USUBJID\", count_by = \"EVENT\") #> $unique #> [1] 3.0 0.6 #> attr(,\"label\") #> [1] \"\" #>  #> $nonunique #> [1] 3 #> attr(,\"label\") #> [1] \"\" #>  #> $unique_count #> [1] 3 #> attr(,\"label\") #> [1] \"(n)\" #>"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze function analyze_patients_exposure_in_cols() creates layout element count total numbers patients sum analysis value (.e. exposure) across patients columns. primary analysis variable ex_var exposure variable used calculate sum_exposure statistic. id variable used uniquely identify patients data unique patients counted n_patients statistic, var variable used create row split needed. percentage returned part n_patients statistic proportion records correspond unique patient. summarize function summarize_patients_exposure_in_cols() performs function analyze_patients_exposure_in_cols() except creates content rows, data rows, summarize current table row/column context operates level latest row split root table row splits occurred. column split yet performed table, col_split must set TRUE first call analyze_patients_exposure_in_cols() summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"analyze_patients_exposure_in_cols(   lyt,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = 0L,   ... )  summarize_patients_exposure_in_cols(   lyt,   var,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   col_split = TRUE,   na_str = default_na_str(),   ...,   .stats = c(\"n_patients\", \"sum_exposure\"),   .labels = c(n_patients = \"Patients\", sum_exposure = \"Person time\"),   .indent_mods = NULL )  s_count_patients_sum_exposure(   df,   ex_var = \"AVAL\",   id = \"USUBJID\",   labelstr = \"\",   .stats = c(\"n_patients\", \"sum_exposure\"),   .N_col,   custom_label = NULL )  a_count_patients_sum_exposure(   df,   var = NULL,   ex_var = \"AVAL\",   id = \"USUBJID\",   add_total_level = FALSE,   custom_label = NULL,   labelstr = \"\",   .N_col,   .stats,   .formats = list(n_patients = \"xx (xx.x%)\", sum_exposure = \"xx\") )"},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"lyt (PreDataTableLayouts) layout analyses added . var (string) single variable name passed rtables requested statistics function. ex_var (string) name variable df containing exposure values. id (string) subject variable name. add_total_level (flag) adds \"total\" level others includes levels constitute split. custom label can set level via custom_label argument. custom_label (string NULL) provided labelstr empty, used label. col_split (flag) whether columns split. Set FALSE required column split done already earlier layout pipe. na_str (string) string used replace NA empty values output. .stats (character) statistics select table. Options : 'n_patients', 'sum_exposure' .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. ... additional arguments lower level functions. df (data.frame) data set containing analysis variables. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .N_col (integer(1)) column-wise N (column count) full column analyzed typically passed rtables. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted data rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. summarize_patients_exposure_in_cols() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted content rows, statistics s_count_patients_sum_exposure() arranged columns, table layout. s_count_patients_sum_exposure() returns named list statistics: n_patients: Number unique patients df. sum_exposure: Sum ex_var across patients df. a_count_patients_sum_exposure() returns formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"analyze_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::analyze_colvars(). summarize_patients_exposure_in_cols(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::split_cols_by_multivar() rtables::summarize_row_groups(). s_count_patients_sum_exposure(): Statistics function counts numbers patients sum exposure across patients. a_count_patients_sum_exposure(): Analysis function used afun rtables::analyze_colvars() within analyze_patients_exposure_in_cols() cfun rtables::summarize_row_groups() within summarize_patients_exposure_in_cols().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"opposed summarize_patients_exposure_in_cols() generates content rows, analyze_patients_exposure_in_cols() generates data rows repeated multiple pages pagination used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/summarize_patients_exposure_in_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count number of patients and sum exposure across all patients in columns — summarize_patients_exposure_in_cols","text":"","code":"set.seed(1) df <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 6), rep(\"ARM B\", 6)),   SEX = c(rep(\"Female\", 6), rep(\"Male\", 6)),   AVAL = as.numeric(sample(seq(1, 20), 12)),   stringsAsFactors = TRUE ) adsl <- data.frame(   USUBJID = c(paste(\"id\", seq(1, 12), sep = \"\")),   ARMCD = c(rep(\"ARM A\", 2), rep(\"ARM B\", 2)),   SEX = c(rep(\"Female\", 2), rep(\"Male\", 2)),   stringsAsFactors = TRUE )  lyt <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE) result <- build_table(lyt, df = df, alt_counts_df = adsl) result #>                                               ARM A                      ARM B                       Total           #>                                       Patients    Person time    Patients    Person time    Patients     Person time #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total patients numbers/person time   6 (100.0%)       46        6 (100.0%)       68        12 (100.0%)       114     #>   Female                             6 (100.0%)       46         0 (0.0%)         0         6 (50.0%)        46      #>   Male                                0 (0.0%)         0        6 (100.0%)       68         6 (50.0%)        68       lyt2 <- basic_table() %>%   split_cols_by(\"ARMCD\", split_fun = add_overall_level(\"Total\", first = FALSE)) %>%   summarize_patients_exposure_in_cols(     var = \"AVAL\", col_split = TRUE,     .stats = \"n_patients\", custom_label = \"some custom label\"   ) %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = FALSE, ex_var = \"AVAL\") result2 <- build_table(lyt2, df = df, alt_counts_df = adsl) result2 #>                       ARM A        ARM B         Total    #>                      Patients     Patients     Patients   #> ————————————————————————————————————————————————————————— #> some custom label   6 (100.0%)   6 (100.0%)   12 (100.0%) #>   Female            6 (100.0%)    0 (0.0%)     6 (50.0%)  #>   Male               0 (0.0%)    6 (100.0%)    6 (50.0%)   lyt3 <- basic_table() %>%   analyze_patients_exposure_in_cols(var = \"SEX\", col_split = TRUE, ex_var = \"AVAL\") result3 <- build_table(lyt3, df = df, alt_counts_df = adsl) result3 #>          Patients    Person time #> ———————————————————————————————— #> Female   6 (50.0%)       46      #> Male     6 (50.0%)       68       # Adding total levels and custom label lyt4 <- basic_table(   show_colcounts = TRUE ) %>%   analyze_patients_exposure_in_cols(     var = \"ARMCD\",     col_split = TRUE,     add_total_level = TRUE,     custom_label = \"TOTAL\"   ) %>%   append_topleft(c(\"\", \"Sex\"))  result4 <- build_table(lyt4, df = df, alt_counts_df = adsl) result4 #>          Patients     Person time #> Sex       (N=12)        (N=12)    #> ————————————————————————————————— #> ARM A    6 (50.0%)        46      #> ARM B    6 (50.0%)        68      #> TOTAL   12 (100.0%)       114      lyt5 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE)  result5 <- build_table(lyt5, df = df, alt_counts_df = adsl) result5 #>                                       Patients     Person time #> —————————————————————————————————————————————————————————————— #> Total patients numbers/person time   12 (100.0%)       114      lyt6 <- basic_table() %>%   summarize_patients_exposure_in_cols(var = \"AVAL\", col_split = TRUE, .stats = \"sum_exposure\")  result6 <- build_table(lyt6, df = df, alt_counts_df = adsl) result6 #>                                      Person time #> ———————————————————————————————————————————————— #> Total patients numbers/person time       114      a_count_patients_sum_exposure(   df = df,   var = \"SEX\",   .N_col = nrow(df),   .stats = \"n_patients\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>   row_name formatted_cell indent_mod row_label #> 1   Female      6 (50.0%)          0    Female #> 2     Male      6 (50.0%)          0      Male"},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers() function creates layout element tabulate estimated effects multiple continuous biomarker variables survival across subgroups, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_biomarkers(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"tabulate_survival_biomarkers(   df,   vars = c(\"n_tot\", \"n_tot_events\", \"median\", \"hr\", \"ci\", \"pval\"),   groups_lists = list(),   control = control_coxreg(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   na_str = default_na_str(),   .indent_mods = 0L )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"df (data.frame) containing analysis variables, returned extract_survival_biomarkers(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_tot: Total number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. control (list) list parameters returned helper function control_coxreg(). label_all please assign label_all parameter within extract_survival_biomarkers() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. na_str (string) string used replace NA empty values output. .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"rtables table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"functions create layout starting data frame contains required statistics. tables typically used input forest plots.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"tabulate_survival_biomarkers(): Table-creating function creates table summarizing biomarker effects survival subgroup.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"contrast tabulate_survival_subgroups() tabulation function start input layout lyt. internally table created combining multiple subtables.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/survival_biomarkers_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate biomarker effects on survival by subgroup — survival_biomarkers_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(\"AVALU\" = adtte_labels[[\"AVALU\"]], \"is_event\" = \"Event Flag\") formatters::var_labels(adtte_f)[names(labels)] <- labels  # Typical analysis of two continuous biomarkers `BMRKR1` and `AGE`, # in multiple regression models containing one covariate `RACE`, # as well as one stratification variable `STRATA1`. The subgroups # are defined by the levels of `BMRKR2`.  df <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   label_all = \"Total Patients\",   data = adtte_f ) df #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1    68           42 858.9952 0.9623210 #> 6       AGE                          Age    68           42 858.9952 1.0360765 #> 7    BMRKR1 Continuous Level Biomarker 1    62           47 727.8043 1.0770946 #> 8       AGE                          Age    62           47 727.8043 1.0009890 #>         lcl      ucl conf_level      pval     pval_label       subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) Total Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) Total Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)            LOW BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)            LOW BMRKR2 #> 5 0.8708694 1.063376       0.95 0.4509368 p-value (Wald)         MEDIUM BMRKR2 #> 6 0.9727439 1.103532       0.95 0.2707796 p-value (Wald)         MEDIUM BMRKR2 #> 7 0.9756250 1.189118       0.95 0.1412524 p-value (Wald)           HIGH BMRKR2 #> 8 0.9678535 1.035259       0.95 0.9541048 p-value (Wald)           HIGH BMRKR2 #>                      var_label row_type #> 1               Total Patients  content #> 2               Total Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  # Here we group the levels of `BMRKR2` manually. df_grouped <- extract_survival_biomarkers(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     biomarkers = c(\"BMRKR1\", \"AGE\"),     strata = \"STRATA1\",     covariates = \"SEX\",     subgroups = \"BMRKR2\"   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #>   biomarker              biomarker_label n_tot n_tot_events   median        hr #> 1    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 2       AGE                          Age   200          141 753.5176 1.0106406 #> 3    BMRKR1 Continuous Level Biomarker 1    70           52 735.4722 0.9905065 #> 4       AGE                          Age    70           52 735.4722 1.0106279 #> 5    BMRKR1 Continuous Level Biomarker 1   138           94 777.8929 0.9801709 #> 6       AGE                          Age   138           94 777.8929 1.0236283 #> 7    BMRKR1 Continuous Level Biomarker 1   200          141 753.5176 1.0010939 #> 8       AGE                          Age   200          141 753.5176 1.0106406 #>         lcl      ucl conf_level      pval     pval_label        subgroup    var #> 1 0.9538978 1.050625       0.95 0.9646086 p-value (Wald)    All Patients    ALL #> 2 0.9871004 1.034742       0.95 0.3787395 p-value (Wald)    All Patients    ALL #> 3 0.9142220 1.073156       0.95 0.8155443 p-value (Wald)             low BMRKR2 #> 4 0.9621192 1.061582       0.95 0.6735773 p-value (Wald)             low BMRKR2 #> 5 0.9235465 1.040267       0.95 0.5094582 p-value (Wald)      low/medium BMRKR2 #> 6 0.9859367 1.062761       0.95 0.2224475 p-value (Wald)      low/medium BMRKR2 #> 7 0.9538978 1.050625       0.95 0.9646086 p-value (Wald) low/medium/high BMRKR2 #> 8 0.9871004 1.034742       0.95 0.3787395 p-value (Wald) low/medium/high BMRKR2 #>                      var_label row_type #> 1                 All Patients  content #> 2                 All Patients  content #> 3 Continuous Level Biomarker 2 analysis #> 4 Continuous Level Biomarker 2 analysis #> 5 Continuous Level Biomarker 2 analysis #> 6 Continuous Level Biomarker 2 analysis #> 7 Continuous Level Biomarker 2 analysis #> 8 Continuous Level Biomarker 2 analysis  ## Table with default columns. tabulate_survival_biomarkers(df) #>                                  Total n   Total Events   Median   Hazard Ratio   95% Wald CI    p-value (Wald) #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Age                                                                                                             #>   Total Patients                   200         141        753.5        1.01       (0.99, 1.03)       0.3787     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        1.01       (0.96, 1.06)       0.6736     #>     MEDIUM                         68           42        859.0        1.04       (0.97, 1.10)       0.2708     #>     HIGH                           62           47        727.8        1.00       (0.97, 1.04)       0.9541     #> Continuous Level Biomarker 1                                                                                    #>   Total Patients                   200         141        753.5        1.00       (0.95, 1.05)       0.9646     #>   Continuous Level Biomarker 2                                                                                  #>     LOW                            70           52        735.5        0.99       (0.91, 1.07)       0.8155     #>     MEDIUM                         68           42        859.0        0.96       (0.87, 1.06)       0.4509     #>     HIGH                           62           47        727.8        1.08       (0.98, 1.19)       0.1413      ## Table with a manually chosen set of columns: leave out \"pval\", reorder. tab <- tabulate_survival_biomarkers(   df = df,   vars = c(\"n_tot_events\", \"ci\", \"n_tot\", \"median\", \"hr\"),   time_unit = as.character(adtte_f$AVALU[1]) )  ## Finally produce the forest plot. # \\donttest{ g_forest(tab, xlim = c(0.8, 1.2))  # }"},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":null,"dir":"Reference","previous_headings":"","what":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"analyze function coxph_pairwise() creates layout element analyze pairwise Cox-PH model. function can return statistics including p-value, hazard ratio (HR), HR confidence intervals stratified unstratified Cox-PH models. variable(s) analyzed specified via vars argument stratification factors via strata argument.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"coxph_pairwise(   lyt,   vars,   strata = NULL,   control = control_coxph(),   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"CoxPH\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"pvalue\", \"hr\", \"hr_ci\"),   .formats = NULL,   .labels = NULL,   .indent_mods = NULL )  s_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )  a_coxph_pairwise(   df,   .ref_group,   .in_ref_col,   .var,   is_event,   strata = NULL,   strat = lifecycle::deprecated(),   control = control_coxph() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . strata (character NULL) variable names indicating stratification factors. control (list) parameters comparison details, specified using helper function control_coxph(). possible parameter options : pval_method (string) p-value method testing null hypothesis hazard ratio = 1. Default method \"log-rank\" comes survival::survdiff(), can also set \"wald\" \"likelihood\" (survival::coxph()). ties (string) specifying method tie handling. Default \"efron\", can also set \"breslow\" \"exact\". See survival::coxph(). conf_level (proportion) confidence level interval HR. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'pvalue', 'hr', 'hr_ci', 'n_tot', 'n_tot_events' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative. df (data.frame) data set containing analysis variables. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise. .var (string) single variable name passed rtables requested statistics function. is_event (flag)TRUE event, FALSE time event censored. strat Please use strata argument instead.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_coxph_pairwise() table layout. s_coxph_pairwise() returns statistics: pvalue: p-value test null hypothesis hazard ratio = 1. hr: Hazard ratio. hr_ci: Confidence interval hazard ratio. n_tot: Total number observations. n_tot_events: Total number events. a_coxph_pairwise() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"coxph_pairwise(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_coxph_pairwise(): Statistics function analyzes HR, CIs HR, p-value Cox-PH model. a_coxph_pairwise(): Formatted analysis function used afun coxph_pairwise().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_coxph_pairwise.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Analyze a pairwise Cox-PH model — survival_coxph_pairwise","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(is_event = CNSR == 0)  df <- adtte_f %>% filter(ARMCD == \"ARM A\") df_ref_group <- adtte_f %>% filter(ARMCD == \"ARM B\")  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Unstratified Analysis\"   ) %>%   build_table(df = adtte_f) #>                         ARM A       ARM B          ARM C     #>                         (N=69)      (N=73)         (N=58)    #> ———————————————————————————————————————————————————————————— #> Unstratified Analysis                                        #>   p-value (log-rank)                0.0905         0.0086    #>   Hazard Ratio                       1.41           1.81     #>   95% CI                         (0.95, 2.09)   (1.16, 2.84)  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   coxph_pairwise(     vars = \"AVAL\",     is_event = \"is_event\",     var_labels = \"Stratified Analysis\",     strata = \"SEX\",     control = control_coxph(pval_method = \"wald\")   ) %>%   build_table(df = adtte_f) #>                       ARM A       ARM B          ARM C     #>                       (N=69)      (N=73)         (N=58)    #> —————————————————————————————————————————————————————————— #> Stratified Analysis                                        #>   p-value (wald)                  0.0784         0.0066    #>   Hazard Ratio                     1.44           1.89     #>   95% CI                       (0.96, 2.15)   (1.19, 2.98)"},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":null,"dir":"Reference","previous_headings":"","what":"Tabulate survival duration by subgroup — survival_duration_subgroups","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups() function creates layout element tabulate survival duration subgroup, returning statistics including median survival time hazard ratio population subgroup. table created df, list data frames returned extract_survival_subgroups(), statistics include specified via vars parameter. forest plot can created resulting table using g_forest() function.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"tabulate_survival_subgroups(   lyt,   df,   vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\"),   groups_lists = list(),   label_all = lifecycle::deprecated(),   time_unit = NULL,   riskdiff = NULL,   na_str = default_na_str(),   .formats = c(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot =     \"xx\", hr = list(format_extreme_values(2L)), ci = list(format_extreme_values_ci(2L)),     pval = \"x.xxxx | (<0.0001)\") )  a_survival_subgroups(   .formats = list(n = \"xx\", n_events = \"xx\", n_tot_events = \"xx\", median = \"xx.x\", n_tot     = \"xx\", hr = list(format_extreme_values(2L)), ci =     list(format_extreme_values_ci(2L)), pval = \"x.xxxx | (<0.0001)\"),   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"lyt (PreDataTableLayouts) layout analyses added . df (list) list data frames containing analysis variables. List created using extract_survival_subgroups(). vars (character) names statistics reported among: n_tot_events: Total number events per group. n_events: Number events per group. n_tot: Total number observations per group. n: Number observations per group. median: Median survival time. hr: Hazard ratio. ci: Confidence interval hazard ratio. pval: p-value effect. Note, one statistics n_tot n_tot_events, well hr ci required. groups_lists (named list list) optionally contains subgroups variable list, specifies new group levels via names levels belong character vectors elements list. label_all please assign label_all parameter within extract_survival_subgroups() function creating df. time_unit (string) label unit median survival time. Default NULL skips displaying unit. riskdiff (list) risk (proportion) difference column added, list settings apply within column. See control_riskdiff() details. NULL, risk difference column added. riskdiff$arm_x riskdiff$arm_y NULL, first level df$survtime$arm used arm_x second level arm_y. na_str (string) string used replace NA empty values output. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"rtables table summarizing survival subgroup. a_survival_subgroups() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"functions create layout starting data frame contains required statistics. Tables typically used part forest plot.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"tabulate_survival_subgroups(): Table-creating function creates table summarizing survival subgroup. function wrapper rtables::analyze_colvars() rtables::summarize_row_groups(). a_survival_subgroups(): Formatted analysis function used afun tabulate_survival_subgroups().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/survival_duration_subgroups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tabulate survival duration by subgroup — survival_duration_subgroups","text":"","code":"library(dplyr)  adtte <- tern_ex_adtte  # Save variable labels before data processing steps. adtte_labels <- formatters::var_labels(adtte)  adtte_f <- adtte %>%   filter(     PARAMCD == \"OS\",     ARM %in% c(\"B: Placebo\", \"A: Drug X\"),     SEX %in% c(\"M\", \"F\")   ) %>%   mutate(     # Reorder levels of ARM to display reference arm before treatment arm.     ARM = droplevels(forcats::fct_relevel(ARM, \"B: Placebo\")),     SEX = droplevels(SEX),     AVALU = as.character(AVALU),     is_event = CNSR == 0   ) labels <- c(   \"ARM\" = adtte_labels[[\"ARM\"]],   \"SEX\" = adtte_labels[[\"SEX\"]],   \"AVALU\" = adtte_labels[[\"AVALU\"]],   \"is_event\" = \"Event Flag\" ) formatters::var_labels(adtte_f)[names(labels)] <- labels  df <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   label_all = \"Total Patients\",   data = adtte_f ) df #> $survtime #>           arm  n n_events    median       subgroup    var #> 1  B: Placebo 73       57  727.8043 Total Patients    ALL #> 2   A: Drug X 69       44  974.6402 Total Patients    ALL #> 3  B: Placebo 40       31  599.1772              F    SEX #> 4   A: Drug X 38       24 1016.2982              F    SEX #> 5  B: Placebo 33       26  888.4916              M    SEX #> 6   A: Drug X 31       20  974.6402              M    SEX #> 7  B: Placebo 24       21  735.4722            LOW BMRKR2 #> 8   A: Drug X 26       15  974.6402            LOW BMRKR2 #> 9  B: Placebo 23       14  731.8352         MEDIUM BMRKR2 #> 10  A: Drug X 26       17  964.2197         MEDIUM BMRKR2 #> 11 B: Placebo 26       22  654.8245           HIGH BMRKR2 #> 12  A: Drug X 17       12 1016.2982           HIGH BMRKR2 #>                       var_label row_type #> 1                Total Patients  content #> 2                Total Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        49           31 0.7651261 0.3641277 1.6077269       0.95 0.47860004 #> 6        43           34 0.6662356 0.3257413 1.3626456       0.95 0.26285846 #>           pval_label       subgroup    var                    var_label #> 1 p-value (log-rank) Total Patients    ALL               Total Patients #> 2 p-value (log-rank)              F    SEX                          Sex #> 3 p-value (log-rank)              M    SEX                          Sex #> 4 p-value (log-rank)            LOW BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)         MEDIUM BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank)           HIGH BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   df_grouped <- extract_survival_subgroups(   variables = list(     tte = \"AVAL\",     is_event = \"is_event\",     arm = \"ARM\", subgroups = c(\"SEX\", \"BMRKR2\")   ),   data = adtte_f,   groups_lists = list(     BMRKR2 = list(       \"low\" = \"LOW\",       \"low/medium\" = c(\"LOW\", \"MEDIUM\"),       \"low/medium/high\" = c(\"LOW\", \"MEDIUM\", \"HIGH\")     )   ) ) df_grouped #> $survtime #>           arm  n n_events    median        subgroup    var #> 1  B: Placebo 73       57  727.8043    All Patients    ALL #> 2   A: Drug X 69       44  974.6402    All Patients    ALL #> 3  B: Placebo 40       31  599.1772               F    SEX #> 4   A: Drug X 38       24 1016.2982               F    SEX #> 5  B: Placebo 33       26  888.4916               M    SEX #> 6   A: Drug X 31       20  974.6402               M    SEX #> 7  B: Placebo 24       21  735.4722             low BMRKR2 #> 8   A: Drug X 26       15  974.6402             low BMRKR2 #> 9  B: Placebo 47       35  735.4722      low/medium BMRKR2 #> 10  A: Drug X 52       32  964.2197      low/medium BMRKR2 #> 11 B: Placebo 73       57  727.8043 low/medium/high BMRKR2 #> 12  A: Drug X 69       44  974.6402 low/medium/high BMRKR2 #>                       var_label row_type #> 1                  All Patients  content #> 2                  All Patients  content #> 3                           Sex analysis #> 4                           Sex analysis #> 5                           Sex analysis #> 6                           Sex analysis #> 7  Continuous Level Biomarker 2 analysis #> 8  Continuous Level Biomarker 2 analysis #> 9  Continuous Level Biomarker 2 analysis #> 10 Continuous Level Biomarker 2 analysis #> 11 Continuous Level Biomarker 2 analysis #> 12 Continuous Level Biomarker 2 analysis #>  #> $hr #>   arm n_tot n_tot_events        hr       lcl       ucl conf_level       pval #> 1       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #> 2        78           55 0.5595391 0.3246658 0.9643271       0.95 0.03411759 #> 3        64           46 0.9102874 0.5032732 1.6464678       0.95 0.75582028 #> 4        50           36 0.7617717 0.3854349 1.5055617       0.95 0.43236030 #> 5        99           67 0.7472958 0.4600419 1.2139136       0.95 0.23764314 #> 6       142          101 0.7108557 0.4779138 1.0573368       0.95 0.09049511 #>           pval_label        subgroup    var                    var_label #> 1 p-value (log-rank)    All Patients    ALL                 All Patients #> 2 p-value (log-rank)               F    SEX                          Sex #> 3 p-value (log-rank)               M    SEX                          Sex #> 4 p-value (log-rank)             low BMRKR2 Continuous Level Biomarker 2 #> 5 p-value (log-rank)      low/medium BMRKR2 Continuous Level Biomarker 2 #> 6 p-value (log-rank) low/medium/high BMRKR2 Continuous Level Biomarker 2 #>   row_type #> 1  content #> 2 analysis #> 3 analysis #> 4 analysis #> 5 analysis #> 6 analysis #>   ## Table with default columns. basic_table() %>%   tabulate_survival_subgroups(df, time_unit = adtte_f$AVALU[1]) #>                                                     B: Placebo               A: Drug X                                      #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI  #> ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06) #> Sex                                                                                                                         #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96) #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65) #> Continuous Level Biomarker 2                                                                                                #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51) #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61) #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)  ## Table with a manually chosen set of columns: adding \"pval\". basic_table() %>%   tabulate_survival_subgroups(     df = df,     vars = c(\"n_tot_events\", \"n_events\", \"median\", \"hr\", \"ci\", \"pval\"),     time_unit = adtte_f$AVALU[1]   ) #>                                                     B: Placebo               A: Drug X                                                           #> Baseline Risk Factors          Total Events   Events   Median (DAYS)   Events   Median (DAYS)   Hazard Ratio   95% Wald CI    p-value (log-rank) #> ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————— #> Total Patients                     101          57         727.8         44         974.6           0.71       (0.48, 1.06)         0.0905       #> Sex                                                                                                                                              #>   F                                 55          31         599.2         24        1016.3           0.56       (0.32, 0.96)         0.0341       #>   M                                 46          26         888.5         20         974.6           0.91       (0.50, 1.65)         0.7558       #> Continuous Level Biomarker 2                                                                                                                     #>   LOW                               36          21         735.5         15         974.6           0.76       (0.39, 1.51)         0.4324       #>   MEDIUM                            31          14         731.8         17         964.2           0.77       (0.36, 1.61)         0.4786       #>   HIGH                              34          22         654.8         12        1016.3           0.67       (0.33, 1.36)         0.2629"},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time analysis — survival_time","title":"Survival time analysis — survival_time","text":"analyze function surv_time() creates layout element analyze survival time calculating survival time median, median confidence interval, quantiles, range (, censored, event patients). primary analysis variable vars time variable secondary analysis variable is_event indicates whether event occurred.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time analysis — survival_time","text":"","code":"surv_time(   lyt,   vars,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   na_str = default_na_str(),   nested = TRUE,   ...,   var_labels = \"Time to Event\",   show_labels = \"visible\",   table_names = vars,   .stats = c(\"median\", \"median_ci\", \"quantiles\", \"range\"),   .formats = NULL,   .labels = NULL,   .indent_mods = c(median_ci = 1L) )  s_surv_time(df, .var, is_event, control = control_surv_time())  a_surv_time(   df,   labelstr = \"\",   .var = NULL,   .df_row = NULL,   is_event,   control = control_surv_time(),   ref_fn_censor = TRUE,   .stats = NULL,   .formats = NULL,   .labels = NULL,   .indent_mods = NULL,   na_str = default_na_str() )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time analysis — survival_time","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_time(). possible parameter options : conf_level (proportion) confidence level interval survival time. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" supported. quantiles (numeric) vector length two specify quantiles survival time. ref_fn_censor (flag) whether referential footnotes indicating censored observations printed range statistic included. na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". table_names (character) can customized case vars analyzed multiple times, avoid warnings rtables. .stats (character) statistics select table. Options : 'median', 'median_ci', 'quantiles', 'range_censor', 'range_event', 'range' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. labelstr (string) label level parent split currently summarized (must present second argument Content Row Functions). See rtables::summarize_row_groups() information. .df_row (data.frame) data frame across columns given row split.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time analysis — survival_time","text":"surv_time() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_time() table layout. s_surv_time() returns statistics: median: Median survival time. median_ci: Confidence interval median time. quantiles: Survival time two specified quantiles. range_censor: Survival time range censored observations. range_event: Survival time range observations events. range: Survival time range observations. a_surv_time() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time analysis — survival_time","text":"surv_time(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_time(): Statistics function analyzes survival times. a_surv_time(): Formatted analysis function used afun surv_time().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time analysis — survival_time","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   ) df <- adtte_f %>% filter(ARMCD == \"ARM A\")  basic_table() %>%   split_cols_by(var = \"ARMCD\") %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",     control = control_surv_time(conf_level = 0.9, conf_type = \"log-log\")   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     90% CI               (22.6, 46.5)   (18.3, 29.2)   (12.9, 25.9) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   a_surv_time(   df,   .df_row = df,   .var = \"AVAL\",   is_event = \"is_event\" ) #> RowsVerticalSection (in_rows) object print method: #> ---------------------------- #>           row_name formatted_cell indent_mod        row_label #> 1           Median           32.0          0           Median #> 2           95% CI   (22.5, 49.3)          0           95% CI #> 3  25% and 75%-ile     17.4, 65.3          0  25% and 75%-ile #> 4 Range (censored)    0.8 to 63.5          0 Range (censored) #> 5    Range (event)   0.3 to 155.5          0    Range (event) #> 6            Range   0.3 to 155.5          0            Range"},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Survival time point analysis — survival_timepoint","title":"Survival time point analysis — survival_timepoint","text":"analyze function surv_timepoint() creates layout element analyze patient survival rates difference survival rates groups given time point. primary analysis variable vars time variable. required inputs time_point, numeric time point interest, is_event, variable indicates whether event occurred. method argument used specify whether want analyze survival estimations (\"surv\"), difference survival control (\"surv_diff\"), (\"\").","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Survival time point analysis — survival_timepoint","text":"","code":"surv_timepoint(   lyt,   vars,   time_point,   is_event,   control = control_surv_timepoint(),   method = c(\"surv\", \"surv_diff\", \"both\"),   na_str = default_na_str(),   nested = TRUE,   ...,   table_names_suffix = \"\",   var_labels = \"Time\",   show_labels = \"visible\",   .stats = c(\"pt_at_risk\", \"event_free_rate\", \"rate_ci\", \"rate_diff\", \"rate_diff_ci\",     \"ztest_pval\"),   .formats = NULL,   .labels = NULL,   .indent_mods = if (method == \"both\") {      c(rate_diff = 1L, rate_diff_ci = 2L,     ztest_pval = 2L)  } else {      c(rate_diff_ci = 1L, ztest_pval = 1L)  } )  s_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  a_surv_timepoint(   df,   .var,   time_point,   is_event,   control = control_surv_timepoint() )  s_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )  a_surv_timepoint_diff(   df,   .var,   .ref_group,   .in_ref_col,   time_point,   control = control_surv_timepoint(),   ... )"},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Survival time point analysis — survival_timepoint","text":"lyt (PreDataTableLayouts) layout analyses added . vars (character) variable names primary analysis variable iterated . time_point (numeric(1)) survival time point interest. is_event (flag)TRUE event, FALSE time event censored. control (list) parameters comparison details, specified using helper function control_surv_timepoint(). possible parameter options : conf_level (proportion) confidence level interval survival rate. conf_type (string) confidence interval type. Options \"plain\" (default), \"log\", \"log-log\", see survival::survfit(). Note option \"none\" longer supported. method (string)\"surv\" (survival estimations), \"surv_diff\" (difference survival control), \"\". na_str (string) string used replace NA empty values output. nested (flag) whether layout instruction applied within existing layout structure _if possible (TRUE, default) new top-level element (FALSE). Ignored nest split. underneath analyses, allowed. ... additional arguments lower level functions. table_names_suffix (string) optional suffix table_names used rtables avoid warnings duplicate table names. var_labels (character) variable labels. show_labels (string) label visibility: one \"default\", \"visible\" \"hidden\". .stats (character) statistics select table. Options : 'pt_at_risk', 'event_free_rate', 'rate_se', 'rate_ci', 'rate_diff', 'rate_diff_ci', 'ztest_pval' .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. element vector name-value pair name corresponding statistic specified .stats value indentation statistic's row label. df (data.frame) data set containing analysis variables. .var (string) single variable name passed rtables requested statistics function. .ref_group (data.frame vector) data corresponding reference group. .in_ref_col (flag)TRUE working reference level, FALSE otherwise.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint() returns layout object suitable passing layouting functions, rtables::build_table(). Adding function rtable layout add formatted rows containing statistics s_surv_timepoint() /s_surv_timepoint_diff() table layout depending value method. s_surv_timepoint() returns statistics: pt_at_risk: Patients remaining risk. event_free_rate: Event-free rate (%). rate_se: Standard error event free rate. rate_ci: Confidence interval event free rate. a_surv_timepoint() returns corresponding list formatted rtables::CellValue(). s_surv_timepoint_diff() returns statistics: rate_diff: Event-free rate difference two groups. rate_diff_ci: Confidence interval difference. ztest_pval: p-value test difference 0. a_surv_timepoint_diff() returns corresponding list formatted rtables::CellValue().","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Survival time point analysis — survival_timepoint","text":"surv_timepoint(): Layout-creating function can take statistics function arguments additional format arguments. function wrapper rtables::analyze(). s_surv_timepoint(): Statistics function analyzes survival rate. a_surv_timepoint(): Formatted analysis function used afun surv_timepoint() method = \"surv\". s_surv_timepoint_diff(): Statistics function analyzes difference two survival rates. a_surv_timepoint_diff(): Formatted analysis function used afun surv_timepoint() method = \"surv_diff\".","code":""},{"path":"https://insightsengineering.github.io/tern/reference/survival_timepoint.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Survival time point analysis — survival_timepoint","text":"","code":"library(dplyr)  adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  # Survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 7   ) %>%   build_table(df = adtte_f) #>                                    ARM A            ARM B            ARM C      #>                                    (N=69)           (N=73)           (N=58)     #> ——————————————————————————————————————————————————————————————————————————————— #> 7 Months                                                                        #>   Patients remaining at risk         54               57               42       #>   Event Free Rate (%)              84.89            79.43            75.50      #>   95% CI                       (76.24, 93.53)   (70.15, 88.71)   (64.33, 86.67)  # Difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"surv_diff\",     .indent_mods = c(\"rate_diff\" = 0L, \"rate_diff_ci\" = 2L, \"ztest_pval\" = 2L)   ) %>%   build_table(df = adtte_f) #>                                   ARM A        ARM B            ARM C      #>                                   (N=69)       (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                   #>   Difference in Event Free Rate                -9.64            -13.03     #>       95% CI                               (-22.80, 3.52)   (-27.59, 1.53) #>       p-value (Z-test)                         0.1511           0.0794      # Survival and difference in survival at given time points. basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM A\") %>%   add_colcounts() %>%   surv_timepoint(     vars = \"AVAL\",     var_labels = \"Months\",     is_event = \"is_event\",     time_point = 9,     method = \"both\"   ) %>%   build_table(df = adtte_f) #>                                       ARM A            ARM B            ARM C      #>                                       (N=69)           (N=73)           (N=58)     #> —————————————————————————————————————————————————————————————————————————————————— #> 9 Months                                                                           #>   Patients remaining at risk            53               53               39       #>   Event Free Rate (%)                 84.89            75.25            71.86      #>   95% CI                          (76.24, 93.53)   (65.32, 85.17)   (60.14, 83.57) #>   Difference in Event Free Rate                        -9.64            -13.03     #>     95% CI                                         (-22.80, 3.52)   (-27.59, 1.53) #>     p-value (Z-test)                                   0.1511           0.0794"},{"path":"https://insightsengineering.github.io/tern/reference/tern-package.html","id":null,"dir":"Reference","previous_headings":"","what":"tern Package — tern-package","title":"tern Package — tern-package","text":"Package create tables, listings graphs analyze clinical trials data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tern-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"tern Package — tern-package","text":"Maintainer: Joe Zhu joe.zhu@roche.com Authors: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Jana Stoilova jana.stoilova@roche.com Davide Garolini davide.garolini@roche.com Emily de la Rua emily.de_la_rua@contractors.roche.com Abinaya Yogasekaram abinaya.yogasekaram@contractors.roche.com Heng Wang wang.heng@gene.com Francois Collin Adrian Waddell adrian.waddell@gene.com Pawel Rucki pawel.rucki@roche.com Chendi Liao chendi.liao@roche.com Jennifer Li li.jing@gene.com contributors: F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for binomial GLM results — tidy.glm","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"Helper method (broom::tidy()) prepare data frame glm object binomial family.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"# S3 method for class 'glm' tidy(x, conf_level = 0.95, at = NULL, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"x (glm) logistic regression model fitted stats::glm() \"binomial\" family. conf_level (proportion) confidence level interval. (numeric NULL) optional values interaction variable. Otherwise median used. ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"data.frame containing tidied model.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy.glm.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for binomial GLM results — tidy.glm","text":"","code":"library(dplyr) library(broom)  adrs_f <- tern_ex_adrs %>%   filter(PARAMCD == \"BESRSPI\") %>%   filter(RACE %in% c(\"ASIAN\", \"WHITE\", \"BLACK OR AFRICAN AMERICAN\")) %>%   mutate(     Response = case_when(AVALC %in% c(\"PR\", \"CR\") ~ 1, TRUE ~ 0),     RACE = factor(RACE),     SEX = factor(SEX)   ) formatters::var_labels(adrs_f) <- c(formatters::var_labels(tern_ex_adrs), Response = \"Response\") mod1 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\")   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred mod2 <- fit_logistic(   data = adrs_f,   variables = list(     response = \"Response\",     arm = \"ARMCD\",     covariates = c(\"AGE\", \"RACE\"),     interaction = \"AGE\"   ) ) #> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred  df <- tidy(mod1, conf_level = 0.99) df2 <- tidy(mod2, conf_level = 0.99)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom tidy method for STEP results — tidy.step","title":"Custom tidy method for STEP results — tidy.step","text":"Tidy STEP results tibble format ready plotting.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"# S3 method for class 'step' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy method for STEP results — tidy.step","text":"x (matrix) results fit_survival_step(). ... used.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy method for STEP results — tidy.step","text":"tibble one row per STEP subgroup. estimates CIs HR scale, respectively. Additional attributes carry metadata also used plotting.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy.step.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy method for STEP results — tidy.step","text":"","code":"library(survival) lung$sex <- factor(lung$sex) vars <- list(   time = \"time\",   event = \"status\",   arm = \"sex\",   biomarker = \"age\" ) step_matrix <- fit_survival_step(   variables = vars,   data = lung,   control = c(control_coxph(), control_step(num_points = 10, degree = 2)) ) broom::tidy(step_matrix) #> # A tibble: 10 × 12 #>    `Percentile Center` `Percentile Lower` `Percentile Upper` `Interval Center` #>  *               <dbl>              <dbl>              <dbl>             <dbl> #>  1              0.0909             0                   0.341              50   #>  2              0.182              0                   0.432              54   #>  3              0.273              0.0227              0.523              57   #>  4              0.364              0.114               0.614              59.5 #>  5              0.455              0.205               0.705              62   #>  6              0.545              0.295               0.795              64   #>  7              0.636              0.386               0.886              67   #>  8              0.727              0.477               0.977              69   #>  9              0.818              0.568               1                  71   #> 10              0.909              0.659               1                  74   #> # ℹ 8 more variables: `Interval Lower` <dbl>, `Interval Upper` <dbl>, n <dbl>, #> #   events <dbl>, `Hazard Ratio` <dbl>, se <dbl>, ci_lower <dbl>, #> #   ci_upper <dbl>"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"# S3 method for class 'summary.coxph' tidy(x, ...)  # S3 method for class 'coxreg.univar' tidy(x, ...)  # S3 method for class 'coxreg.multivar' tidy(x, ...)"},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"x (list) result Cox regression model fitted fit_coxreg_univar() (univariate models) fit_coxreg_multivar() (multivariate models). ... additional arguments lower level functions.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"broom::tidy() returns: summary.coxph objects,  data.frame columns: Pr(>|z|), exp(coef), exp(-coef), lower .95, upper .95, level, n. coxreg.univar objects, data.frame columns: effect, term, term_label, level, n, hr, lcl, ucl, pval, ci. coxreg.multivar objects, data.frame columns: term, pval, term_label, hr, lcl, ucl, level, ci.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"tidy(summary.coxph): Custom tidy method survival::coxph() summary results. Tidy survival::coxph() results data.frame extract model results. tidy(coxreg.univar): Custom tidy method univariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_univar(). tidy(coxreg.multivar): Custom tidy method multivariate Cox regression. Tidy result Cox regression model fitted fit_coxreg_multivar().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/tidy_coxreg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom tidy methods for Cox regression — tidy_coxreg","text":"","code":"library(survival) library(broom)  set.seed(1, kind = \"Mersenne-Twister\")  dta_bladder <- with(   data = bladder[bladder$enum < 5, ],   data.frame(     time = stop,     status = event,     armcd = as.factor(rx),     covar1 = as.factor(enum),     covar2 = factor(       sample(as.factor(enum)),       levels = 1:4, labels = c(\"F\", \"F\", \"M\", \"M\")     )   ) ) labels <- c(\"armcd\" = \"ARM\", \"covar1\" = \"A Covariate Label\", \"covar2\" = \"Sex (F/M)\") formatters::var_labels(dta_bladder)[names(labels)] <- labels dta_bladder$age <- sample(20:60, size = nrow(dta_bladder), replace = TRUE)  formula <- \"survival::Surv(time, status) ~ armcd + covar1\" msum <- summary(coxph(stats::as.formula(formula), data = dta_bladder)) tidy(msum) #>       Pr(>|z|) exp(coef) exp(-coef)  lower .95 upper .95   level   n #> 1 1.287954e-02 0.6110123   1.636628 0.41442417 0.9008549  armcd2 340 #> 2 6.407916e-04 0.4460731   2.241785 0.28061816 0.7090818 covar12 340 #> 3 5.272933e-06 0.3075864   3.251119 0.18517346 0.5109230 covar13 340 #> 4 2.125359e-08 0.1808795   5.528541 0.09943722 0.3290258 covar14 340  ## Cox regression: arm + 1 covariate. mod1 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = \"covar1\"   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91) )  ## Cox regression: arm + 1 covariate + interaction, 2 candidate covariates. mod2 <- fit_coxreg_univar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder,   control = control_coxreg(conf_level = 0.91, interaction = TRUE) )  tidy(mod1) #>            effect   term        term_label level   n        hr       lcl #> ref    Treatment:  armcd  2 vs control (1)     2 340 0.6386426 0.4557586 #> covar1 Covariate: covar1 A Covariate Label     2 340  0.607037 0.4324571 #>              ucl       pval                   ci #> ref    0.8949131 0.02423805 0.4557586, 0.8949131 #> covar1 0.8520935 0.01257339 0.4324571, 0.8520935 tidy(mod2) #>                           effect   term        term_label level   n        hr #> ref                   Treatment:  armcd  2 vs control (1)     2 340 0.6386426 #> covar1.1              Covariate: covar1 A Covariate Label       340           #> covar1.armcd2/covar11 Covariate: covar1                 1     1     0.6284569 #> covar1.armcd2/covar12 Covariate: covar1                 2     2     0.5806499 #> covar1.armcd2/covar13 Covariate: covar1                 3     3     0.5486103 #> covar1.armcd2/covar14 Covariate: covar1                 4     4     0.6910725 #> covar2.1              Covariate: covar2         Sex (F/M)       340           #> covar2.armcd2/covar2F Covariate: covar2                 F     F     0.6678243 #> covar2.armcd2/covar2M Covariate: covar2                 M     M     0.5954021 #>                             lcl       ucl       pval pval_inter #> ref                   0.4557586 0.8949131 0.02423805            #> covar1.1                     NA        NA             0.9883021 #> covar1.armcd2/covar11 0.3450471 1.1446499                       #> covar1.armcd2/covar12 0.2684726 1.2558239                       #> covar1.armcd2/covar13 0.2226814 1.3515868                       #> covar1.armcd2/covar14 0.2308006 2.0692373                       #> covar2.1                     NA        NA             0.7759013 #> covar2.armcd2/covar2F 0.3649842 1.2219413                       #> covar2.armcd2/covar2M 0.3572772 0.9922368                       #>                                         ci #> ref                   0.4557586, 0.8949131 #> covar1.1                                   #> covar1.armcd2/covar11 0.3450471, 1.1446499 #> covar1.armcd2/covar12 0.2684726, 1.2558239 #> covar1.armcd2/covar13 0.2226814, 1.3515868 #> covar1.armcd2/covar14 0.2308006, 2.0692373 #> covar2.1                                   #> covar2.armcd2/covar2F 0.3649842, 1.2219413 #> covar2.armcd2/covar2M 0.3572772, 0.9922368  multivar_model <- fit_coxreg_multivar(   variables = list(     time = \"time\", event = \"status\", arm = \"armcd\",     covariates = c(\"covar1\", \"covar2\")   ),   data = dta_bladder ) broom::tidy(multivar_model) #>                       term         pval                        term_label #> armcd.1              armcd                            ARM (reference = 1) #> armcd.2                ARM   0.01232761                                 2 #> covar1.1            covar1 7.209956e-09 A Covariate Label (reference = 1) #> covar1.2 A Covariate Label  0.001120332                                 2 #> covar1.3 A Covariate Label 6.293725e-06                                 3 #> covar1.4 A Covariate Label 3.013875e-08                                 4 #> covar2.1            covar2                      Sex (F/M) (reference = F) #> covar2.2         Sex (F/M)    0.1910521                                 M #>                 hr        lcl       ucl level                     ci #> armcd.1                    NA        NA  <NA>                        #> armcd.2  0.6062777 0.40970194 0.8971710     2   0.4097019, 0.8971710 #> covar1.1                   NA        NA  <NA>                        #> covar1.2 0.4564763 0.28481052 0.7316115     2   0.2848105, 0.7316115 #> covar1.3 0.3069612 0.18386073 0.5124813     3   0.1838607, 0.5124813 #> covar1.4 0.1817017 0.09939435 0.3321668     4 0.09939435, 0.33216684 #> covar2.1                   NA        NA  <NA>                        #> covar2.2  1.289373 0.88087820 1.8873019     M   0.8808782, 1.8873019"},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":null,"dir":"Reference","previous_headings":"","what":"Replicate entries of a vector if required — to_n","title":"Replicate entries of a vector if required — to_n","text":"Replicate entries vector required.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replicate entries of a vector if required — to_n","text":"","code":"to_n(x, n)"},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replicate entries of a vector if required — to_n","text":"x (numeric) vector numbers want analyze. n (integer(1)) number entries needed.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replicate entries of a vector if required — to_n","text":"x required length already NULL, otherwise scalar replicated version n entries.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_n.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Replicate entries of a vector if required — to_n","text":"function fail x length n /scalar.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert table into matrix of strings — to_string_matrix","title":"Convert table into matrix of strings — to_string_matrix","text":"Helper function use mostly within tests. with_spacesparameter allows test content also indentation table structure. print_txt_to_copy instead facilitate testing development returning well formatted text needs copied pasted expected output.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"to_string_matrix(   x,   widths = NULL,   max_width = NULL,   hsep = formatters::default_hsep(),   with_spaces = TRUE,   print_txt_to_copy = FALSE )"},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert table into matrix of strings — to_string_matrix","text":"x (VTableTree)rtables table object. widths (numeric  NULL) Proposed widths columns x. expected length numeric vector can retrieved ncol(x) + 1 column row names must also considered. max_width (integer(1), string NULL) width title footer (including footnotes) materials word-wrapped . NULL, set current print width session (getOption(\"width\")). set \"auto\", width table (plus table inset) used. Parameter ignored tf_wrap = FALSE. hsep (string) character repeat create header/body separator line. NULL, object value used. \" \", empty separator printed. See default_hsep() information. with_spaces (flag) whether tested table keep indentation relevant spaces. print_txt_to_copy (flag) utility way copy input table directly expected variable instead copying manually.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert table into matrix of strings — to_string_matrix","text":"matrix strings. print_txt_to_copy = TRUE well formatted printout table printed console, ready copied expected value.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/to_string_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert table into matrix of strings — to_string_matrix","text":"","code":"tbl <- basic_table() %>%   split_rows_by(\"SEX\") %>%   split_cols_by(\"ARM\") %>%   analyze(\"AGE\") %>%   build_table(tern_ex_adsl)  to_string_matrix(tbl, widths = ceiling(propose_column_widths(tbl) / 2)) #>  [1] \"       A:                    \" \"      Drug    B: Pl   C: Comb\" #>  [3] \"        X     acebo   ination\" \"—————————————————————————————\" #>  [5] \"F                            \" \"  M   33.68   35.98    36.02 \" #>  [7] \"  e                          \" \"  a                          \" #>  [9] \"  n                          \" \"M                            \" #> [11] \"  M   34.70   35.68    36.28 \" \"  e                          \" #> [13] \"  a                          \" \"  n                          \""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":null,"dir":"Reference","previous_headings":"","what":"tryCatch around car::Anova — try_car_anova","title":"tryCatch around car::Anova — try_car_anova","text":"Captures warnings executing car::Anova.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"try_car_anova(mod, test.statistic)"},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"tryCatch around car::Anova — try_car_anova","text":"mod lm, aov, glm, multinom, polr     mlm, coxph, coxme, lme, mer, merMod, svyglm, svycoxph,     rlm, clm, clmm, suitable model object. test.statistic generalized linear model, whether calculate     \"LR\" (likelihood-ratio), \"Wald\", \"F\" tests; Cox     Cox mixed-effects model, whether calculate \"LR\" (partial-likelihood ratio)     \"Wald\" tests (\"LR\" tests unavailable Cox models using tt argument); default case linear mixed models fit     lmer, whether calculate Wald \"Chisq\" Kenward-Roger     \"F\" tests Satterthwaite degrees freedom (warning: KR F-tests     can time-consuming).     multivariate linear model, multivariate test statistic compute — one     \"Pillai\", \"Wilks\", \"Hotelling-Lawley\", \"Roy\",     \"Pillai\" default. summary method Anova.mlm     objects permits specification one multivariate     test statistic, default report four.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"tryCatch around car::Anova — try_car_anova","text":"list item aov result model error_text captured warnings.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/try_car_anova.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"tryCatch around car::Anova — try_car_anova","text":"","code":"# `car::Anova` on cox regression model including strata and expected # a likelihood ratio test triggers a warning as only Wald method is # accepted.  library(survival)  mod <- coxph(   formula = Surv(time = futime, event = fustat) ~ factor(rx) + strata(ecog.ps),   data = ovarian )"},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":null,"dir":"Reference","previous_headings":"","what":"Ungroup non-numeric statistics — ungroup_stats","title":"Ungroup non-numeric statistics — ungroup_stats","text":"Ungroups grouped non-numeric statistics within input vectors .formats, .labels, .indent_mods.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Ungroup non-numeric statistics — ungroup_stats","text":"","code":"ungroup_stats(x, .formats, .labels, .indent_mods)"},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Ungroup non-numeric statistics — ungroup_stats","text":"x (named list numeric) list numeric statistics containing statistics ungroup. .formats (named character list) formats statistics. See Details analyze_vars information \"auto\" setting. .labels (named character) labels statistics (without indent). .indent_mods (named integer) indent modifiers labels. Defaults 0, corresponds unmodified default behavior. Can negative.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/ungroup_stats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Ungroup non-numeric statistics — ungroup_stats","text":"list modified elements x, .formats, .labels, .indent_mods.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":null,"dir":"Reference","previous_headings":"","what":"Univariate formula special term — univariate","title":"Univariate formula special term — univariate","text":"special term univariate indicate model fitted individually every variable included univariate.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Univariate formula special term — univariate","text":"","code":"univariate(x)"},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Univariate formula special term — univariate","text":"x (character) vector variable names separated commas.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Univariate formula special term — univariate","text":"used within model formula, produces univariate models variable provided.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/univariate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Univariate formula special term — univariate","text":"provided alongside pairwise specification, model y ~ ARM + univariate(SEX, AGE, RACE) lead study comparison models y ~ ARM y ~ ARM + SEX y ~ ARM + AGE y ~ ARM + RACE","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Blank for missing input — unlist_and_blank_na","title":"Blank for missing input — unlist_and_blank_na","text":"Helper function use tabulating model results.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Blank for missing input — unlist_and_blank_na","text":"","code":"unlist_and_blank_na(x)"},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Blank for missing input — unlist_and_blank_na","text":"x (vector) input cell.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/unlist_and_blank_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Blank for missing input — unlist_and_blank_na","text":"empty character vector entries x missing (NA), otherwise unlisted version x.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"function wraps iteration procedure allows estimate weights proportional strata. assumes minimize weighted squared length confidence interval.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"update_weights_strat_wilson(   vars,   strata_qnorm,   initial_weights,   n_per_strata,   max_iterations = 50,   conf_level = 0.95,   tol = 0.001 )"},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"vars (numeric) normalized proportions strata. strata_qnorm (numeric(1)) initial estimation identical weights quantiles. initial_weights (numeric) initial weights used calculate strata_qnorm. can optimized future need estimate better initial weights. n_per_strata (numeric) number elements strata. max_iterations (integer(1)) maximum number iterations tried. Convergence always checked. conf_level (proportion) confidence level interval. tol (numeric(1)) tolerance threshold convergence.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"list 3 elements: n_it, weights, diff_v.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/update_weights_strat_wilson.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper function for the estimation of weights for prop_strat_wilson() — update_weights_strat_wilson","text":"","code":"vs <- c(0.011, 0.013, 0.012, 0.014, 0.017, 0.018) sq <- 0.674 ws <- rep(1 / length(vs), length(vs)) ns <- c(22, 18, 17, 17, 14, 12)  update_weights_strat_wilson(vs, sq, ws, ns, 100, 0.95, 0.001) #> $n_it #> [1] 3 #>  #> $weights #> [1] 0.2067191 0.1757727 0.1896962 0.1636346 0.1357615 0.1284160 #>  #> $diff_v #> [1] 1.458717e-01 1.497223e-03 1.442189e-06 #>"},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Custom split functions — utils_split_funs","title":"Custom split functions — utils_split_funs","text":"Collection useful functions expanding core list functions provided rtables. See rtables::custom_split_funs rtables::make_split_fun() information make custom split function. functions work rtables::split_rows_by() argument split_fun modify way split happens. split functions, consider consulting rtables::split_funcs.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Custom split functions — utils_split_funs","text":"","code":"ref_group_position(position = \"first\")  level_order(order)"},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Custom split functions — utils_split_funs","text":"position (string integer) position use reference group facet. Can \"first\", \"last\", specific position. order (character numeric) vector ordering indices split facets.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Custom split functions — utils_split_funs","text":"ref_group_position() returns utility function puts reference group first, last certain position needs assigned split_fun. level_order() returns utility function changes original levels' order, depending input order split levels.","code":""},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Custom split functions — utils_split_funs","text":"ref_group_position(): Split function place reference group facet specific position post-processing stage. level_order(): Split function change level order based integer vector character vector represent split variable's factor levels.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/reference/utils_split_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Custom split functions — utils_split_funs","text":"","code":"library(dplyr)  dat <- data.frame(   x = factor(letters[1:5], levels = letters[5:1]),   y = 1:5 )  # With rtables layout functions basic_table() %>%   split_cols_by(\"x\", ref_group = \"c\", split_fun = ref_group_position(\"last\")) %>%   analyze(\"y\") %>%   build_table(dat) #>         e      d      b      a      c   #> ——————————————————————————————————————— #> Mean   5.00   4.00   2.00   1.00   3.00  # With tern layout funcitons adtte_f <- tern_ex_adtte %>%   filter(PARAMCD == \"OS\") %>%   mutate(     AVAL = day2month(AVAL),     is_event = CNSR == 0   )  basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(\"first\")) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM B          ARM A          ARM C     #>                             (N=73)         (N=69)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     23.9           32.0           20.8     #>     95% CI               (18.3, 32.9)   (22.5, 49.3)   (12.9, 26.0) #>   25% and 75%-ile         9.8, 42.0      17.4, 65.3     7.3, 37.1   #>   Range                  0.1 to 154.1   0.3 to 155.5   0.6 to 80.7   basic_table() %>%   split_cols_by(var = \"ARMCD\", ref_group = \"ARM B\", split_fun = ref_group_position(2)) %>%   add_colcounts() %>%   surv_time(     vars = \"AVAL\",     var_labels = \"Survival Time (Months)\",     is_event = \"is_event\",   ) %>%   build_table(df = adtte_f) #>                             ARM A          ARM B          ARM C     #>                             (N=69)         (N=73)         (N=58)    #> ——————————————————————————————————————————————————————————————————— #> Survival Time (Months)                                              #>   Median                     32.0           23.9           20.8     #>     95% CI               (22.5, 49.3)   (18.3, 32.9)   (12.9, 26.0) #>   25% and 75%-ile         17.4, 65.3     9.8, 42.0      7.3, 37.1   #>   Range                  0.3 to 155.5   0.1 to 154.1   0.6 to 80.7   # level_order -------- # Even if default would bring ref_group first, the original order puts it last basic_table() %>%   split_cols_by(\"Species\", split_fun = level_order(c(1, 3, 2))) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94     # character vector new_order <- level_order(levels(iris$Species)[c(1, 3, 2)]) basic_table() %>%   split_cols_by(\"Species\", ref_group = \"virginica\", split_fun = new_order) %>%   analyze(\"Sepal.Length\") %>%   build_table(iris) #>        setosa   virginica   versicolor #> —————————————————————————————————————— #> Mean    5.01      6.59         5.94"},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-6-9006","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6.9006","text":"Fixed bug a_summary() causing non-unique row_name values occur multiple statistics selected count variables.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-096","dir":"Changelog","previous_headings":"","what":"tern 0.9.6","title":"tern 0.9.6","text":"CRAN release: 2024-09-24","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.6","text":"Added errorbar_width linetype parameters g_lineplot. Added .formats argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users specify formats. Added riskdiff argument tabulate_rsp_subgroups tabulate_survival_subgroups allow users add risk difference table column, function control_riskdiff specify settings risk difference column. Added warning tabulate_rsp_subgroups pval statistic selected df correctly generated add p-values output table. Added n_rate statistic non-default option estimate_incidence_rate returns number events observed estimated incidence rate. Added n_unique statistic non-default option estimate_incidence_rate returns total number patients least one event observed. Refactored estimate_incidence_rate work analyze function summarize function, controlled added summarize parameter. summarize = TRUE, labels can fine-tuned via new label_fmt argument function. Added fraction statistic analyze_var_count method group. Improved summarize_glm_count() documentation associated functions better describe results functions’ purpose. Added method argument s_odds_ratio() estimate_odds_ratio() control whether exact approximate conditional likelihood calculations used.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-6","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.6","text":"Added defaults d_count_cumulative parameters described documentation. Fixed bug empty levels g_lineplot x-axis shown either plots. Fixed bug a_surv_time threw error split \"is_event\". Fixed disappearing line g_lineplot using one group strata level. Fixed defaults formats labels get_formats_from_stats get_labels_from_stats. Fixed bug linear scaling factor (scale parameter) applied response rate h_glm_count distributions logarithmic link function. Fixed bug decorate_grob handle well empty strings NULL values title footers. Fixed bug g_km caused error multiple records data estimates max time. Fixed issue wrong wrapping due different \\n vector behavior cope well split_string().","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.6","text":"Began deprecation confusing functions summary_formats summary_labels. Enhanced general descriptions analyze summarize functions throughout package documentation. Finalized deprecation strata cohort_id arguments g_lineplot. Moved incidence rate helper functions separate h_incidence_rate.R file.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-095","dir":"Changelog","previous_headings":"","what":"tern 0.9.5","title":"tern 0.9.5","text":"CRAN release: 2024-06-21","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.5","text":"Added facet_var g_lineplot allow plot faceting factor variable. Added examples tests label_all parameter extract_survival_biomarkers extract_survival_subgroups. Added xticks, xlim, ylim arguments g_lineplot allow customization x y axes. Updated g_lineplot legend follow factor levels set users.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.5","text":"Fixed bug s_ancova prevented statistics printed arm levels include special characters. Fixed bug decorate_grob prevented right margins respected adding title footers decorations.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.5","text":"Began deprecation unused label_all parameter tabulate_survival_biomarkers tabulate_survival_subgroups, redirection parameter associated extract_* functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-094","dir":"Changelog","previous_headings":"","what":"tern 0.9.4","title":"tern 0.9.4","text":"CRAN release: 2024-04-17","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-4","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.4","text":"Added h_glm_negbin h_glm_count enable count data analysis using negative binomial model. Added argument grade_groups_only count_occurrences_by_grade allow users display rows specified grade groups. Added internal function df2gg converts data.frame objects ggplot objects. Added functions control_surv_med_annot control_coxph_annot configure g_km annotation table sizes/positions. Refactored g_km output ggplot object instead grob object. Refactored g_forest output ggplot object instead grob object.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.4","text":"Default format mean p-values (mean_pval) updated \"xx.xx\" \"x.xxxx | (<0.0001)\".","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.4","text":"Fixed nested column split label overlay issue rtable2gg clean appearance text labels. Fixed bug s_ancova causing incorrect difference calculations arm variables irregular levels. Fixed bug format_count_fraction_fixed_dp print fraction 1 (100%). Fixed bug g_lineplot causing default labels update according specified control settings. Fixed bug causing error automatic value formatting applied NA values.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.4","text":"Added function expect_snapshot_ggplot test setup file process plot snapshot tests allow plot dimensions set. Adapted argument renames introduced ggplot2 3.5.0. Renamed individual_patient_plot.R g_ipp.R. Removed instances deprecated parameters time_unit_input, time_unit_output, na_level indent_mod. Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, summary_custom. Removed vdiffr package Suggests DESCRIPTION file. Began deprecation named element strat, renamed strata, within variables argument h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, extract_survival_subgroups. Began deprecation strat argument s_coxph_pairwise replaced strata argument. Began deprecation forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, grid.forest functions. Began deprecation longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, h_grob_coxph. Began deprecation grob/grid related functions stack_grobs, arrange_grobs, draw_grob longer used tern.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-093","dir":"Changelog","previous_headings":"","what":"tern 0.9.3","title":"tern 0.9.3","text":"CRAN release: 2023-12-08","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.3","text":"Added ref_group_position function place reference group facet last, first certain position. Added keep_level_order split function retain original order levels split. Added level_order split function reorder manually levels. Added function get_indents_from_stats format return indent modifiers given set statistics. Added internal utility function apply_auto_formatting check \"auto\" formats replace implementation format_auto analyze functions. Added utility function labels_use_control modify labels control specifications. Added list containing default statistics method group, tern_default_stats. Added summarize function version count_occurrences analyze function, summarize_occurrences. Added referential footnotes surv_time censored range observations, controlled via ref_fn_censor parameter. Added helper function h_adlb_abnormal_by_worst_grade prepare ADLB data use input count_abnormal_by_worst_grade. Added s_bland_altman function assess agreement two numerical vectors. Added function rtable2gg converts rtable objects ggplot objects. Added helper function set default na_str globally set_default_na_str() added default_na_str() interested functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.3","text":"Added ref_group_coxph parameter g_km specify reference group used pairwise Cox-PH calculations annot_coxph = TRUE. Added annot_coxph_ref_lbls parameter g_km enable printing reference group table labels annot_coxph = TRUE. Added x_lab parameter g_lineplot customize x-axis label. Remove 25% padding y-axis g_lineplot. Added support creating multiple risk difference columns, comparing single comparison group. Multiple comparison groups can specified vector via arm_y argument. Allowed numeric vector count_by input analyze_num_patients summarize_num_patients. Aligned plot table vertically g_lineplot.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.3","text":"Fixed bug decorate_grob preventing text wrapping accounting font size. Fixed implementation na_str argument column-wise analysis tabulation functions.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.3","text":"Specified minimal version package dependencies. Upgraded to_string_matrix take account widths printing parameters.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-2","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.2","text":"Added na_str argument analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.2","text":"Added formatting function format_count_fraction_lt10 formatting count_fraction special consideration count less 10. Updated s_summary.logical output count_fraction denominator zero display NA instead 0 tables. Updated analyze_vars_in_cols allow character input indicate whether nominal time point post-dose pre-dose applying 1/3 imputation rule.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.2","text":"Fixed bug g_km causing error converting certain annotation width units.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.2","text":"Began deprecation na_level argument s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, summarize_coxreg replaced na_str argument. strata cohort_id parameters renamed group_var subject_var respectively g_lineplot control_lineplot_vars .","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-1","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.1","text":"Added imputation_rule function apply imputation rule data. Added new format function format_sigfig allow numeric value formatting specified number significant figures. Added vectors containing default statistic formats labels tern_default_formats tern_default_labels, respectively. Added function get_stats return methods given statistical method groups. Added function get_formats_from_stats return formats get_labels_from_stats return labels given set statistics. Added \"auto\" option .formats. uses format_auto determine automatically number digits. Added title argument h_grob_tbl_at_risk annot_at_risk_title argument g_km h_km_layout allows user add “Patients Risk” title Kaplan-Meier risk annotation table.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-1","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.1","text":"Refactored tabulate_rsp_subgroups pass sanitation checks preventing creation degenerate subtables. Updated analyze_vars_in_cols use caching, allow implementation imputation rule via imp_rule argument, allow user specify cell alignment via .aligns argument. Updated add_rowcounts allow addition row counts alt_counts_df using alt_counts argument. Added gp argument g_forest control graphical parameters font size.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.1","text":"Grouped functions relating valid method names default formats labels new source file utils_defaults_handling.R. Started deprecation summary_custom() a_summary() S3 method. Renamed statistical method p-value discrete case pval_counts. Removed a_summary_internal() favor one main a_summary().","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-090","dir":"Changelog","previous_headings":"","what":"tern 0.9.0","title":"tern 0.9.0","text":"CRAN release: 2023-09-01","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-9-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.9.0","text":"Added stat_propdiff_ci function calculate proportion/risk difference CI. Added risk difference column functionality via riskdiff argument functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, summarize_num_patients.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-9-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.9.0","text":"Refactored function a_summary longer use helper function create_afun_summary. Refactored functions summarize_vars compare_vars use refactored a_summary function. Created new internal helper functions ungroup_stats ungroup statistics calculated factor variables, a_summary_internal perform calculations a_summary.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-9-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.9.0","text":"Fixed bug s_count_occurrences_by_grade “missing” grade always appears final level. Fixed bug analyze_vars_in_cols categorical data used. Fixed bug s_count_occurrences_by_grade levels relabeled reordering account “missing” grades.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-9-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.9.0","text":"Fixed swapped descriptions .N_row .N_col parameters. Removed internal calls df_explicit_na. Changes NA values happen externally tern functions, depending users’ needs. Reinstated correct soft deprecation create_afun_summary create_afun_compare.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.5","text":"Added ylim argument g_km allow user set custom limits y-axis. Added assertion g_km checks whether one arm present data annot_coxph true. Added flag_labels argument s_count_patients_with_flags enable label handling options count_patients_by_flags. Added nested argument analyze wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, estimate_incidence_rate, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, analyze_num_patients, coxph_pairwise, surv_time, surv_timepoint.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.5","text":"Started deprecation cycle summarize_vars control_summarize_vars. Renamed analyze_vars control_analyze_vars reflect underlying rtables machinery keeping backward compatibility aliases.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-084","dir":"Changelog","previous_headings":"","what":"tern 0.8.4","title":"tern 0.8.4","text":"CRAN release: 2023-06-27","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.4","text":"Added method character class h_coxreg_inter_effect enabling character covariates summarize_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.4","text":"Began deprecation time_unit_input time_unit_output arguments replaced input_time_unit num_pt_year, respectively, control_incidence_rate. Removed deprecated pairwise function. Deprecated a_compare replaced a_summary argument compare = TRUE. Deprecated helper functions create_afun_summary create_afun_compare longer used a_summary a_compare respectively.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.4","text":"Fixed long double assertion check sum(weights) M1mac installation.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-083","dir":"Changelog","previous_headings":"","what":"tern 0.8.3","title":"tern 0.8.3","text":"CRAN release: 2023-06-19","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.3","text":"Added explicit zero counts g_km plot “risk” annotation tables. Added flag total level split analyze_patients_exposure_in_cols. Implemented .indent_mods argument functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, cfun_by_flag. Updated summarize_coxreg print covariates data rows univariate Cox regression interactions content rows otherwise. Removed “baseline status” text d_count_abnormal_by_baseline labels. Improved default sizing annotation tables g_km added dynamic scaling surv_med coxph annotation tables, customization via width_annots argument.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.3","text":"Fixed bug split_text_grob preventing titles footnotes properly formatted printed decorate_grob. Fixed bug g_lineplot preventing addition lines plot midpoint statistic calculations result NA value(s). Fixed tern:::tidy.glm formals respect broom:::tidy.default formals.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.3","text":"Updated README include installation instructions CRAN. Remove examples unexported functions. Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport. Updated README include installation instructions CRAN. Began deprecation indent_mod argument replaced .indent_mods argument summarize_num_patients analyze_num_patients.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"breaking-changes-0-8-2","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"tern 0.8.2","text":"Refactored s_coxreg summarize_coxregto work new analysis function a_coxreg.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-2","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.2","text":"Added section_div na_level arguments summarize_vars. Added median_range numeric variable statistic option summarize_vars. Corrected ordering factor levels d_onco_rsp_label. Added new “Analyze Functions”, “Summarize Functions”, “Analyze Functions Columns” overview pages. Consolidated KM plot documentation within g_km function. Added a_count_patients_sum_exposure summarize_patients_exposure_in_cols new analyze function analyze_patients_exposure_in_cols. Added informative error user selects invalid method unstratified analyses s_proportion_diff. Updated s_summary s_compare allow NA values input variables. factor variables NAs, na.rm = FALSE explicit NA level automatically added. na.rm = TRUE also consider \"<Missing>\" values exclude . Updated purpose na_level parameter s_summary s_compare align tern functions. Instead string consider NA setting na.rm = TRUE, now defines string print place NA values output table.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-2","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.2","text":"Fixed missing label TRTEDTM tern datasets. Fixed improper implementation na_level argument summarize_vars preventing effect.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-2","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.2","text":"Implemented lubridate package date variables tern datasets. Organized .gitignore .Rbuildignore files. Removed deprecated footnotes functions related files. Started deprecation cycle pairwise function. Moved count_patients_with_flags functions count_patients_with_event.R count_patients_with_flags.R.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-8-0","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.8.0","text":"Added summarize_glm_count function analyze count data using linear model. Added legend g_step. Added formatting functions format_fraction_fixed_dp format_count_fraction_fixed_dp fixed single decimal place percentages. Added na_level labelstr arguments summarize_vars_in_cols. Added analyze_num_patients include summary beginning repeat paginating. Added h_row_first_values function general helper function retrieve first values specific rows. Added option remove \"(n)\" suffix unique_count labels s_num_patients. Added options g_km annotate statistics (annot_stats) add corresponding vertical lines (annot_stats_lines).","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-8-0","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.8.0","text":"Fixed bug causing incorrect ordering numeric grade levels missing grades present s_count_occurrences_by_grade. Refactored summarize_vars_in_cols work pagination machinery. Fixed bug allow passing conf_level argument emmeans::contrast() s_ancova. Fixed bugs rtables_access.R caused checking specific combinations (also standard values never used) column indices names. Fixed single applicable record bug count_abnormal_by_grade. Fixed bug add_rowcounts caused row count row values count zero. Fixed bug h_col_indices causing error pruning combination columns. Fixed bug test_proportion_diff missing argument var_labels.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-tests-0-8-0","dir":"Changelog","previous_headings":"","what":"Documentation and Tests","title":"tern 0.8.0","text":"Added tests increase code coverage. Created separate documentation files functions different sections pkgdown reference. Created separate .R files logistic regression cox regression helper functions. Fixed table tests using analyze_num_patients generate initial summary repetition paginating. Updated tests use testthat 3rd edition replaced applicable tests snapshot testing. Updated summarize_ancova examples use iris dataset instead scda data. Created vignette saves cached synthetic CDISC dataset files data/ folder generated cached synthetic datasets. Updated examples/tests use datasets data/ folder instead scda datasets. Removed template tests tern. tests internal repo scda.test.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-8-0","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.8.0","text":"Renamed summarize_vars_in_cols analyze_vars_in_cols reflect appropriate analyze logic. Removed redundant summary_in_cols helper functions. Exported function format_xx. Replaced deprecated ggplot2 functions/arguments fix warnings. Replaced deprecated function forcats::fct_explicit_na forcats::fct_na_value_to_level. Removed deprecated wrap_text function related files. Started deprecation cycle footnotes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-10","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.10","text":"Added stratified Newcombe stratified Wilson statistics estimate_proportion estimate_proportion_diff relative tests. Added stat_mean_pval, new summary statistic calculate p-value mean. Added statistic mean_se (mean standard error) summarize_variables related functions. Introduced Rdpack references.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-10","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.10","text":"Redesign data handling tests removing repetitive data loads library calls. Added DescTools::BinomDiffCI function within tern. Added new parameter summarize_logistic specify pivoted value use analysis. Updated s_coxph_pairwise generate log-rank p-value using original log-rank test instead Cox Proportional-Hazards Model. Implemented nestcolor examples adapting g_km, g_ipp, g_waterfall, g_step, g_lineplot, g_forest. Added parameters interaction_y interaction_item ANCOVA make interaction calculations available. Added new parameter footnotes add footnotes g_km.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"migration-from-assertthat-to-checkmate-0-7-10","dir":"Changelog","previous_headings":"","what":"Migration from assertthat to checkmate","title":"tern 0.7.10","text":"Implemented checkmate::assert_vector, checkmate::assert_set_equal, checkmate::assert_int check vector type, length, values. Replaced standard assertions checkmate following functions: all_elements_in_ref, is_df_with_nlevels_factor, is_df_with_no_na_level, is_proportion_vector, is_quantiles_vector, is_character_or_factor, is_nonnegative_count, is_valid_character, assert_character_or_factor, assert_equal_length has_tabletree_colnames. Modified is_proportion, is_equal_length, is_df_with_no_na_level, is_df_with_nlevels_factor, is_variables, is_df_with_variables, is_df_with_factors, is_valid_factor use assertion logic. Added verbose warnings as_factor_keep_attributes. Made assert_df_with_factors assert_proportion_value internal functions. Renamed assertthat.R test-assertthat.R utils_checkmate.R test-utils_checkmate.R.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-namespace-polishing-0-7-10","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE Polishing","title":"tern 0.7.10","text":"count_abnormal_by_marked (reference abnormal_by_marked), count_abnormal_lab_worsen_by_baseline h_adlb_worsen (reference abnormal_by_worst_grade_worsen_from_baseline), count_abnormal_by_worst_grade (reference abnormal_by_worst_grade), to_string_matrix, tidy.summary.coxph, tidy.step, surv_timepoint, (reference survival_timepoint), surv_time (reference survival_time), coxph_pairwise (reference survival_coxph_pairwise), extract_survival_subgroups tabulate_survival_subgroups (reference survival_duration_subgroups), extract_survival_biomarkers tabulate_survival_biomarkers (reference survival_biomarkers_subgroups), control_summarize_vars, s_summary a_summary (reference summarize_variables) kept S3 method tree. summarize_patients_exposure_in_cols, summarize_num_patients s_num_patients, s_num_patients_content, summarize_num_patients. count_cumulative, count_missed_doses, count_patients_events_in_cols, summarize_colvars, summarize_change, summarize_ancova,.rtable, color_palette, add_footnotes. (statistical function controls) control_coxreg, control_coxph, control_incidence_rate, control_lineplot_vars, control_surv_time, control_surv_timepoint, control_logisitic, control_step. stat_mean_ci, stat_median_ci, split_cols_by_groups, explicit_na, sas_na, extract_rsp_subgroups, tabulate_rsp_subgroups, extract_rsp_biomarkers, tabulate_rsp_biomarkers, keep_rows, keep_content_rows, has_count_in_any_col, has_fraction_in_cols, has_fraction_in_any_col, has_fractions_difference, test_proportion_diff, pairwise, logistic_regression, estimate_incidence_rate, control_incidence_rate (reference incidence_rate), cut_quantile_bins, estimate_multinomial_rsp, decorate_grob_set, extreme_format, fit_rsp_step, fit_survival_step, footnotes, footnotes-set, format_count_fraction, format_fraction_threshold, formatting_functions, format_fraction, combination_function (S4 method), compare_variables (S3 method), kaplan_meier. (chain functions, reference abnormal_by_marked) s_count_abnormal_by_marked, a_count_abnormal_by_marked. (chain functions, reference abnormal_by_worst_grade_worsen_from_baseline) a_count_abnormal_lab_worsen_by_baseline, s_count_abnormal_lab_worsen_by_baseline. (chain functions, reference abnormal_by_worst_grade) s_count_abnormal_by_worst_grade, a_count_abnormal_by_worst_grade. (chain functions, reference survival_timepoint) s_surv_timepoint, s_surv_timepoint_diff, a_surv_timepoint, a_surv_timepoint_diff. (chain functions, reference survival_time) s_surv_time, a_surv_time. (chain functions, reference survival_coxph_pairwise) s_coxph_pairwise, a_coxph_pairwise. (chain functions, reference survival_duration_subgroups) a_survival_subgroups. (chain functions, reference count_cumulative) s_count_cumulative, a_count_cumulative. (chain functions, reference count_missed_doses) s_count_nonmissing, s_count_missed_doses, a_count_missed_doses. (chain functions, reference count_patients_events_in_cols) s_count_patients_and_multiple_events, summarize_patients_events_in_cols. (chain functions, reference incidence_rate) s_incidence_rate, a_incidence_rate. (cox regression helper) cox_regression_inter, decorate_grob_factory, draw_grob, estimate_coef. summary_labels, summary_formats, s_count_patients_sum_exposure, a_change_from_baseline s_change_from_baseline, a_ancova, s_ancova, arrange_grobs, as_factor_keep_attributes, combine_levels, split_text_grob, groups_list_to_df, s_cox_multivariate, is_leaf_table, a_response_subgroups, range_noinf, has_count_in_cols, has_counts_difference, prop_chisq, prop_cmh, prop_schouten, prop_fisher, s_test_proportion_diff, a_test_proportion_diff, fct_discard, fct_explicit_na_if.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-10","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.10","text":"Fixed retrieval method stats::ancova output due version inconsistency. Fixed tests respect new standard print NA coming rtables. Fixed error tests coming changes formatters::var_labels. Fixed prop_diff functions respect success responses (TRUE values). Fixed error coming comparing factors vector characters vector. Fixed empty vector exception cut_quantile_bins. Fixed exception error empty strings present pivoted columns (rtables split functions) Fixed bug s_ancova causing error first level arm factor control arm. Fixed bug s_abnormal_by_worst_grade one PARAM level. Fixed bug prop_diff_wald selecting responders, updated tests accordingly. Fixed bug h_ancova caused error deselecting covariates.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-10","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.10","text":"Added deprecated badge g_mmrm. Removed internal function calls examples (tern:::) added dontrun internal function examples. Removed warnings messages console occurring examples tests. Deprecated functions color_palette h_set_nest_theme favor nestcolor::color_palette nestcolor::theme_nest, respectively. Removed deprecated functions: color_palette, color_palette_core, h_set_nest_theme, s_cox_univariate. Removed deprecated MMRM functions: fit_mmrm, g_mmrm_diagnostic, g_mmrm_lsmeans, .rtable.mmrm, h_mmrm_fixed, h_mmrm_cov, h_mmrm_diagnostic, tidy.mmrm, s_mmrm_lsmeans, s_mmrm_lsmeans_single, summarize_lsmeans. Renamed functions arm study_arm extract extract_by_name. Renamed rtables.R utils_rtables.R. Extracted cox_regression_inter separate file cox_regression. Renamed estimate_incidence_rate.R incidence_rate.R match documentation grouping name. Extracted control_incidence_rate separate file produces separate documentation file. Added @md removed @order incidence_rate.R. Modified examples accordingly. Removed hyperlink prop_schouten function documentation. Exported draw_grob function.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"fix-0-7-8","dir":"Changelog","previous_headings":"","what":"Fix","title":"tern 0.7.8","text":"h_split_by_subgroups documentation warning fix wrong placing example block","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"documentation-and-namespace-polishing-0-7-8","dir":"Changelog","previous_headings":"","what":"Documentation and NAMESPACE polishing","title":"tern 0.7.8","text":"Adopting standard badges @description instead every @descriptionIn function. Corrected accordingly summarize_variables_in_cols Added stable badge g_lineplot, g_step, g_waterfall, cox_regression, score_occurrences, add_rowcounts, odds_ratio, count_occurrences, count_occurrences_by_grade, explicit_na, df_explicit_na, count_patients_with_event, decorate_grob, combine_groups, append_varlabels, univariate, stack_grobs, count_abnormal (reference abnormal), count_abnormal_by_baseline (reference abnormal_by_baseline). (helper functions) h_format_row, h_map_for_count_abnormal (utils functions) make_names, month2day, day2month empty_vector_if_na, aesi_label, n_available, format_xx, arm. count_values_funs, prop_difference, combine_counts. (chain functions) s_count_abnormal, a_count_abnormal. (chain functions) s_count_abnormal_by_baseline, a_count_abnormal_by_baseline, d_count_abnormal_by_baseline. Deprecated s_cox_univariate function now deprecated badge.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-8","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.8","text":"Enhanced g_lineplot table automatically scale table height return ggplot object. Enhanced g_ipp caption argument adjust position. Enhanced prop_diff, tern function related functions able apply continuity correction Newcombe method. Enhanced summarize_numeric_in_columns summarize_variables allow factor/character summary able summarize number BLQs AVALC ADPC dataset. Updated order summarize variables stats manual order consistency. Added sum option summarize_variables. Use consistent color palette plotting (stream default). Enhanced h_pkparam_sort function argument key_var allow data different column names.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-8","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.8","text":"Updated test-table_aet02.R variant 12. Changed scda data version ‘2022-02-28’. Added template pkgdown site. Removed package dependencies grDevices, stringr, viridisLite. Renaming summarize_numeric_in_columns summarize_variables_in_columns. Renaming summarize_vars_numeric_in_cols summarize_vars_in_cols. Fixed bug points g_lineplot plot connected missing values. Updated package authors.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"breaking-changes-0-7-7","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"tern 0.7.7","text":"Move MMRM separate package tern.mmrm.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-7","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.7","text":"Added h_pkparam_sort order PK PARAM value based order dataset generated d_pkparam(). Added d_pkparam generate PK parameter map sorting.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-7","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.7","text":"Changed nudge_y argument h_g_ipp dependent data, fixing issue whereby baseline labels offset incorrectly. Enhanced stat_mean_ci s_summary.numeric calculate geometric mean confidence intervals.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-7","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.7","text":"Updated dependencies internal adjustments rtables package refactor. Removed with_label, var_labels, var_labels<- resolve conflict formatters package, new dependency. Added new “Introduction tern” “tern tabulation” vignettes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-6","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.6","text":"Added h_map_for_count_abnormal create map used trim_levels_to_map split function calling helper function. supports two methods: one observed mapping, one least low limit zero least one non missing high limit. Added s_summary_numeric_in_cols summarize_vars_numeric_in_cols functions generate summary statistics columns, mainly used PK datasets. Added five statistics s_summary.numeric use s_summary_numeric_in_cols.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-6","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.6","text":"Enhanced functions tabulate_survival_subgroups tabulate_rsp_subgroups (Survival Duration Best Response analyses) calculate N-s based records considered create model. Enhanced function estimate_proportion related functions able apply continuity correction Wilson method. Refactored count_abnormal_by_marked related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal_by_worst_grade related statistics formatting functions use efficient layout .spl_context argument used determining denominators trim_levels_to_map split function split_rows_by show desired levels table. breaking change. Refactored count_abnormal function related statistics formatting functions use efficient layout trim_levels_to_map split function split_rows_by show desired levels table. Also updated abnormal argument able consider one level direction. breaking change. Enhanced function estimate_incidence_rate related functions consider week time unit data input.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-6","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"tern 0.7.6","text":"Fixed bug assertthat functions output wrong data frame names limited length failure message outputs.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-6","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.6","text":"Removed dependency utils.nest using checkmate purrr packages validation moved get_free_cores skip_if_too_deep functions utils.nest tern.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-5","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.5","text":"Added functions estimate continuous biomarker effects across subgroups survival binary response endpoints, used produce corresponding forest plots, see survival_biomarkers_subgroups response_biomarkers_subgroups. Added g_lineplot plot function, including new h_format_row helper function control_lineplot_vars function. Removed g_summary_by. Added new safety helper function h_stack_by_baskets stack events SMQ /CQ basket flag ADAE data set.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-5","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.5","text":"Added couple new statistics s_summary.numeric. Added names attribute element final list returned s_summary.numeric function. Added summary_formats summary_labels helper functions. Added option also convert logical variables factor variables df_explicit_na. Refactored h_append_grade_groups improve flexibility, robustness clearness, make sure result ordering according order grade_groups. Also, added remove_single argument controls whether elements one-element grade groups output removed. Added var_labels show_labels arguments count_occurrences count_patients_with_flags allow creation title row. Added na_level argument count_abnormal_by_baseline. Updated h_append_grade_groups longer fill-empty grade groups zeros.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.5","text":"Fixed prop_diff_cmh handle edge case FALSE (TRUE) responses. Enhanced g_mmrm_diagnostic improve error handling data amenable Locally Weighted Scatterplot Smoothing. Plot can now display combination annotation tables number patients risk, median survival time, Cox-PH summary. Function return warning instead error arm variable includes single level annot_coxph = TRUE. Lines plot now start time 0 probability 1. Category labels can include equals sign.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.5","text":"Fixed day2month month2day work NA data. Added parameters stat_mean_ci stat_median_ci may return different outputs. Added functionality h_row_counts handle analysis rows NULL cells. Updated LICENCE README new package references. Added error_on_lint: TRUE .lintr.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-4","dir":"Changelog","previous_headings":"","what":"New features","title":"tern 0.7.4","text":"count_abnormal_by_marked tabulates marked laboratory abnormalities. summarize_patients_exposure_in_cols tabulates patient counts sum exposure across patients.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-4","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.4","text":"Enhanced MMRM-related functions fitting models without arm variable. Updated cox_regression work without covariates. Also case interaction model summary, p-values main effect coefficients longer displayed. Descriptive statistics returned summarize_vars now include quantiles. summarize_vars now accepts control function control_summarize_vars specify details confidence level mean median quantile details. control argument replaces conf_level. Added var_labels show_labels arguments count_occurrences_by_grade. Changed indent argument append_varlabels accept non-negative integer represent indent space defined user. Previous calls Boolean indent integer conversion produce warning.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-4","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.4","text":"Corrected tabulate_survival_subgroups related survival forest plot functions use total number events, instead observations, default scaling symbol sizes plot. (user might still use total number observations manually wish .) Helper function h_adsl_adlb_merge_using_worst_flag now impute BTOXGR missing visits.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-4","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.4","text":"Deleted count_abnormal_by_worst_grade_by_baseline related statistic analysis functions simpler design create lab abnormality tables. Switched data examples use scda instead random.cdisc.data package.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-features-0-7-3","dir":"Changelog","previous_headings":"","what":"New Features","title":"tern 0.7.3","text":"Added Subgroup Treatment Effect Pattern (STEP) model fitting functions fit_rsp_step fit_survival_step, corresponding tidy method tidy.step well graph function g_step. Added new layout function compare_vars compares variables different types columns produces p-value comparison reference column. Function built top summarize_vars functionality. cut_quantile_bins cuts numeric vector quantile bins. fct_collapse_only collapses levels factor keeps order provided. fct_explicit_na_if inserts explicit missings factor based condition. range_noinf kind wrapper function base::range. returns c(NA, NA) instead c(-Inf, Inf) zero-length data.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"enhancements-0-7-3","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"tern 0.7.3","text":"Cox regression via fit_coxreg_univar fit_coxreg_multivar now also possible without treatment arm. univariate case means fits separate univariate models provided covariates tabulation corresponding effect estimates can later occur. Added fraction result returned s_count_occurrences. contains list numerators denominators one element per occurrence. Updated sum_num_patients count_occurrences result unique count_fraction return (0, 0) input empty. Added new argument groups_lists extract_survival_subgroups, extract_rsp_subgroups associated helper functions allows group factor levels subgroup variables manually defined groups, enhancing flexibility resulting forest graphs. Forest graph function g_forest now extracts default arguments attributes input table produced tabulate_rsp_subgroups tabulate_survival_subgroups user manually anymore. Remove arm variable name arm labels plot legend annotation tables. Show symbol used mark censored cases match order arm variable factor levels legend. Display hazard ratio confidence interval two decimal places. Updated default position hazard ratio table stay left bottom corner x-axis. Use arm value strata name treatment arm variable single level. Updated s_surv_time function use newly created function range_noinf instead base::range. New argument no_fillin_visits added h_adsl_adlb_merge_using_worst_flag specify excluded visits post-baseline worst toxicity grade output. Improved h_adsl_adlb_merge_using_worst_flag include variables shared adsl adlb, along PARAM, PARAMCD, ATOXGR, BTOXGR optionally AVISIT, AVISITN by_visit = TRUE. Prior output contained USUBJID, ARMCD, PARAMCD, ATOXGR, BTOXGR.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"bug-fixes-0-7-3","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"tern 0.7.3","text":"Fix bug s_surv_timepoint cases zero patients risk. Modified stat_median_ci function passing empty var empty name, row names contain missing values error show.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"miscellaneous-0-7-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"tern 0.7.3","text":"Deprecated s_cox_univariate function, use fit_coxreg_univar function instead. Updated default formats hr hr_ci a_coxph_pairwise median s_surv_time align STREAM. Updated pre-processing code files test-table_ttet01.R test-table_dort01.R make sure analysis variable EVNT1 levels factor defined. Improved error message number levels factor variable data frame expected.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-072","dir":"Changelog","previous_headings":"","what":"tern 0.7.2","title":"tern 0.7.2","text":"Fixed column label internal test errors.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-071","dir":"Changelog","previous_headings":"","what":"tern 0.7.1","title":"tern 0.7.1","text":"New argument position_surv_med added g_km move position annotation table median survival times. Fixed bug g_km related ignored arguments pch size passed helper function h_ggkm. Updated xticks max_time arguments g_km greater functionality. max_time added argument h_xticks allow . Fixed bug prop_diff_cmh led NaN weighted proportion difference estimates missing confidence intervals. change, including patients one treatment arm least one stratum estimation lead numeric results. Fixed bug prop_cmh giving error case least one stratum containing less two observations. New argument n_events added estimate_incidence_rate. New argument denom added count_occurrences. New arguments yval ci_ribbon added g_km. Add new individual patient plot function g_ipp along helpers h_g_ipp h_set_nest_theme. Fixed bug count_patients_with_events, now shows zero counts without percentage. Fixed bug get_mmrm_lsmeans allow MMRM analysis 3000 observations. Updated stat_mean_ci stat_median_ci handle edge cases number elements input series equal 1. cases, NA_real_ now returned, instead NA +/-Inf confidence interval (CI) estimates. Rename n_lim argument stat_mean_ci n_min better reflect desired meaning.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-070","dir":"Changelog","previous_headings":"","what":"tern 0.7.0","title":"tern 0.7.0","text":"version tern introduces major rewriting tern due change layout based tabulation rtables. tern now build tables directly anymore, instead provides analysis functions build tables, see examples. * Counting patients abnormal values post-baseline count_abnormal. * Counting patients graded abnormal values count_abnormal_by_worst_grade. * Counting patients abnormal values baseline status count_abnormal_by_baseline. * Counting patients missed doses s_count_missed_doses count_missed_doses. * Counting patients event flags count_patients_with_event count_patients_with_flags. * Summarizing variables summarize_vars (supports numeric, factor, character logical variables). Note factors need NAs converted na_level use. * Summarizing change baseline summarize_change. * Summarizing variables columns summarize_colvars. * Estimating difference responder proportions estimate_proportion_diff. * Estimating difference Odds Ratio estimate_odds_ratio. * Testing difference responder proportions test_proportion_diff. * Estimating responder proportion level factor estimate_multinomial_response. * Fitting tabulating results Cox regressions fit_coxreg_univar, fit_coxreg_multivar summarize_coxreg, respectively. * Pruning occurrence tables (tables counts fractions) flexible rules, see ?prune_occurrences details. * Sorting occurrence tables using different options, see ?score_occurrences details. * Fitting tabulating MMRM models fit_mmrm .rtable summarize_lsmeans, see ?tabulate_mmrm details. * Counting number unique non-unique patients summarize_num_patients. * Counting occurrences count_occurrences. * Counting occurrences grade summarize_occurrences_by_grade count_occurrences_by_grade. * Counting patients events columns summarize_patients_events_in_cols. * Tabulating binary outcome response subgroup extract_rsp_subgroups tabulate_rsp_subgroups. * Tabulating survival duration subgroup extract_survival_subgroups tabulate_survival_subgroups.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-069","dir":"Changelog","previous_headings":"","what":"tern 0.6.9","title":"tern 0.6.9","text":"Removing used imports.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-068","dir":"Changelog","previous_headings":"","what":"tern 0.6.8","title":"tern 0.6.8","text":"Improved handling missing data aggregation functions: a_mean_sd, a_median, a_n_true_and_freq, a_count, a_q1q3, a_iqr, a_range. New default p-value method s_test_proportion_diff: Chi-Squared Test Schouten Correction. Add new function t_contingency contingency tables. Renamed class splitText dynamicSplitText resolve name conflict package ggpubr. Add rreplace_format tabulation post-processing. Add new tern function t_ancova create ANCOVA tables, well corresponding elementary table function t_el_ancova summary function s_ancova. Add new tern function s_odds_ratio estimate Odds Ratio response categories, well corresponding elementary table function t_el_odds_ratio. Added new CI methods (agresti-coull, jeffreys) s_proportion. Added new CI methods anderson-hauck newcombe s_proportion_diff. Added new p-value methods (Fisher’s Exact, Chi-Squared Test Schouten Correction) s_test_proportion_diff. binary summary table function t_binary_outcome takes now lists (instead character vectors) specified helper function control_binary_comparison arguments strat_analysis unstrat_analysis. Odds Ratio estimates CIs now removable included default, similarly subsections arm comparison analyses. Also added argument rsp_multinomial. Add new table function t_el_multinomial_proportion. Add new table function t_abn_shift. Add new MMRM analysis function s_mmrm, well corresponding table functions t_mmrm_lsmeans, t_mmrm_cov, t_mmrm_diagnostic, t_mmrm_fixed, plot functions g_mmrm_lsmeans, g_mmrm_diagnostic. results match SAS results (numeric precision). Deprecated old MMRM functions a_mmrm t_mmrm (give deprecation warning still work) remove next release. reason results functions don’t match SAS results. Fix bug g_km related numbers patients risk table correct numbers integer time--event variable inputs.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-067","dir":"Changelog","previous_headings":"","what":"tern 0.6.7","title":"tern 0.6.7","text":"functions row_by argument, inputs longer require use nested_by. Add stat_mean_ci stat_median_ci error bars ggplot2. Add new tern function t_coxreg single interface diverse cox regression types. Add compound table binary endpoint: t_binary_endpoint elementary functions: t_el_proportion, t_el_proportion_diff t_el_test_proportion_diff. supporting summary functions added : s_proportion, s_adj_proportion_diff, s_proportion_diff s_test_proportion_diff. Added new tern function t_events_patyear create event table adjusted person-years. Added new tern function t_abnormality elementary table function t_el_abnormality. Removed grade_levels argument t_events_term_grade_id functions. Post-processing reordering leaves table tree creates different ordering rows required. Creating helper function occur later time. Added prune_zero_rows argument t_events_per_term_grade_id t_max_grade_per_id show rows zeros can clutter visualization Shiny app make slower. Fixed position (N=xx) t_summary_by output summarizing numeric columns parallel compare_in_header. Rename t_coxph t_coxph_pairwise reflect model process, add details documentation. Remove test.nest dependency. Keep column labels splitting data tree.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-066","dir":"Changelog","previous_headings":"","what":"tern 0.6.6","title":"tern 0.6.6","text":"Remove test.nest dependency.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-065","dir":"Changelog","previous_headings":"","what":"tern 0.6.5","title":"tern 0.6.5","text":"Change default option denominator N t_summary. Fix IQR bug: IQR Q3 minus Q1. Add new function t_logistic multi-variable logistic regression table. Add new function df_explicit_na replace NA explicit values. Added possibility t_tte specify confidence level independent survfit, coxph, ztest, see manual. Fixed bug t_rsp showing p-value, odds ratio CIs strata_data NULL. Added stratified analysis t_forest_rsp t_forest_tte, footnotes g_forest. Added footnotes, footnotes<- add_footnotes<- functions deal footnotes. Added argument conf_int confidence interval level t_el_forest_rps, t_forest_rsp, t_el_forest_tte, t_forest_tte. Added argument col_symbol_size g_forest control relative size symbols used plot. Added s_coxph_pairwise function perform pairwise testing, used t_tte t_coxph. Added methods t_count_true replacing t_summary_true. Updated t_count_unique create analysis subsets, added t_el_count_unique vectors. Fixed bug t_events_term_id table sort order decreasing frequency instead alphabetical. Added function color_palette new nest color palette.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-064","dir":"Changelog","previous_headings":"","what":"tern 0.6.4","title":"tern 0.6.4","text":"Refactored renaming functions utils.nest. Added event_type argument t_events_per_term_grade_id. Added one/two-arm t-test functions. Improvements t_summary_by. Internal code refactoring.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-063","dir":"Changelog","previous_headings":"","what":"tern 0.6.3","title":"tern 0.6.3","text":"related tree functions see reference trees. Moved label functions rtables. Deleted keys keys<- functions. Exported tabulate_pairwise. get_N, col_N_add_total, check_id. na_as_level. as_factor_keep_attributes. r_by. Disposition elementary table t_el_disposition. t_el_forest_tte, t_el_forest_rsp. Added table_tree argument returns node object. Added f_numeric choose statistics calculate. denominator now also allows omit wanting omit percentages. Renamed row_by. Changed functionality group_data using row_by_list. Removed na_omit_group. Removed indent argument, use indent function rtables. instead","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-062","dir":"Changelog","previous_headings":"","what":"tern 0.6.2","title":"tern 0.6.2","text":"Use cached data random.cdisc.data speed testing. Added t_summary.Date method. Added save_join.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-061","dir":"Changelog","previous_headings":"","what":"tern 0.6.1","title":"tern 0.6.1","text":"Fixed colors Kaplan-Meier Plot Changed width_row.names argument g_forest function width_row_names. Changed censor.show argument g_km function censor_show. Changed col.legend.title argument g_waterfall function col_legend_title. Changed na.rm argument t_count_unique function na_rm. Changed row.name argument t_count_unique function row_name. Changed na.omit.group argument t_forest_rsp function na_omit_group. Changed na.omit.group argument t_forest_tte function na_omit_group. Changed row.name.TRUE row.name.FALSE arguments t_summary.logical row_name_true row_name_false respectively. Rename splotTextGrob split_text_grob. Fix examples. Refactor internal functions code.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-060","dir":"Changelog","previous_headings":"","what":"tern 0.6.0","title":"tern 0.6.0","text":"Removed functions addTable, t_summarize_by_visit, t_summarize_variables. Added t_summary_by function. Refactor g_km function, renamed kmGrob kmCurveGrob. Refactor t_events_* family functions. Updated examples.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-tlgs-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New TLGs","title":"tern 0.5.0.3","text":"t_summary methods data.frame, numeric, logical, character, factor, Date objects. t_events_per_term_id, t_events_per_term_grade_id: Adverse Events & Concomitant Treatment Tables. t_max_grade_per_id, t_count_unique, t_events_summary elementary tables used Adverse Events & Concomitant Treatment Tables. g_waterfall: Horizontal Waterfall Plot.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"new-helper-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"New Helper Functions","title":"tern 0.5.0.3","text":"decorate_grob, decorate_grob_set, decorate_grob_factory, splitTextGrob. stack_grobs, arrange_grobs, draw_grob.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tlg-changes-0-5-0-3","dir":"Changelog","previous_headings":"","what":"TLG changes","title":"tern 0.5.0.3","text":"t_tte now shows two rows ranges event censored times, respectively. g_km works one arm survfit objects. forest plot functions, added formatting display extreme values “>999.9”. t_summarise_variables uses now n instead N denominator calculating percentages factors default. t_rsp now works response values TRUE FALSE.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"deprecated-functions-0-5-0-3","dir":"Changelog","previous_headings":"","what":"Deprecated Functions","title":"tern 0.5.0.3","text":"Deprecated t_summarize_variables t_summary powerful. Replacing t_summarize_by_visit t_summary_by occur upcoming release.","code":""},{"path":"https://insightsengineering.github.io/tern/news/index.html","id":"tern-050","dir":"Changelog","previous_headings":"","what":"tern 0.5.0","title":"tern 0.5.0","text":"First version harmonized analysis functions names arguments.","code":""}]