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Fix documentation for the label_all argument of extract_* functions #1232

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Apr 23, 2024
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Fix documentation for the label_all argument of extract_* functions #1232

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83225ca
Fix documentation for the `label_all` argument of extract functions
edelarua Apr 19, 2024
8a1c056
[skip style] [skip vbump] Restyle files
github-actions[bot] Apr 19, 2024
f05bf5f
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edelarua Apr 19, 2024
2d0c261
Fix lint
edelarua Apr 19, 2024
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6 changes: 6 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# tern 0.9.4.9000

### Enhancements
* Added examples and tests for `label_all` parameter to `extract_survival_biomarkers` and `extract_survival_subgroups`.

### Miscellaneous
* Began deprecation of the unused `label_all` parameter to `tabulate_survival_biomarkers` and `tabulate_survival_subgroups`, with redirection to the same parameter in their associated `extract_*` functions.

# tern 0.9.4

### New Features
Expand Down
18 changes: 16 additions & 2 deletions R/survival_biomarkers_subgroups.R
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Expand Up @@ -53,6 +53,7 @@
#' covariates = "SEX",
#' subgroups = "BMRKR2"
#' ),
#' label_all = "Total Patients",
#' data = adtte_f
#' )
#' df
Expand Down Expand Up @@ -162,6 +163,9 @@ extract_survival_biomarkers <- function(variables,
#' @describeIn survival_biomarkers_subgroups Table-creating function which creates a table
#' summarizing biomarker effects on survival by subgroup.
#'
#' @param label_all `r lifecycle::badge("deprecated")`\cr please assign the `label_all` parameter within the
#' [extract_survival_biomarkers()] function when creating `df`.
#'
#' @return An `rtables` table summarizing biomarker effects on survival by subgroup.
#'
#' @note In contrast to [tabulate_survival_subgroups()] this tabulation function does
Expand Down Expand Up @@ -192,16 +196,26 @@ tabulate_survival_biomarkers <- function(df,
vars = c("n_tot", "n_tot_events", "median", "hr", "ci", "pval"),
groups_lists = list(),
control = control_coxreg(),
label_all = "All Patients",
label_all = lifecycle::deprecated(),
time_unit = NULL,
na_str = default_na_str(),
.indent_mods = 0L) {
if (lifecycle::is_present(label_all)) {
lifecycle::deprecate_warn(
"0.9.5", "tabulate_survival_biomarkers(label_all)",
details = paste(
"Please assign the `label_all` parameter within the",
"`extract_survival_biomarkers()` function when creating `df`."
)
)
}

checkmate::assert_data_frame(df)
checkmate::assert_character(df$biomarker)
checkmate::assert_character(df$biomarker_label)
checkmate::assert_subset(vars, get_stats("tabulate_survival_biomarkers"))

extra_args <- list(groups_lists = groups_lists, control = control, label_all = label_all)
extra_args <- list(groups_lists = groups_lists, control = control)

df_subs <- split(df, f = df$biomarker)
tabs <- lapply(df_subs, FUN = function(df_sub) {
Expand Down
20 changes: 16 additions & 4 deletions R/survival_duration_subgroups.R
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Expand Up @@ -28,7 +28,6 @@
#'
#' @examples
#' library(dplyr)
#' library(forcats)
#'
#' adtte <- tern_ex_adtte
#'
Expand All @@ -43,7 +42,7 @@
#' ) %>%
#' mutate(
#' # Reorder levels of ARM to display reference arm before treatment arm.
#' ARM = droplevels(fct_relevel(ARM, "B: Placebo")),
#' ARM = droplevels(forcats::fct_relevel(ARM, "B: Placebo")),
#' SEX = droplevels(SEX),
#' AVALU = as.character(AVALU),
#' is_event = CNSR == 0
Expand All @@ -62,6 +61,7 @@
#' is_event = "is_event",
#' arm = "ARM", subgroups = c("SEX", "BMRKR2")
#' ),
#' label_all = "Total Patients",
#' data = adtte_f
#' )
#' df
Expand Down Expand Up @@ -199,6 +199,10 @@ a_survival_subgroups <- function(.formats = list( # nolint start
#' summarizing survival by subgroup. This function is a wrapper for [rtables::analyze_colvars()]
#' and [rtables::summarize_row_groups()].
#'
#' @param label_all `r lifecycle::badge("deprecated")`\cr please assign the `label_all` parameter within the
#' [extract_survival_subgroups()] function when creating `df`.
#'
#'
#' @return An `rtables` table summarizing survival by subgroup.
#'
#' @examples
Expand All @@ -220,13 +224,21 @@ tabulate_survival_subgroups <- function(lyt,
df,
vars = c("n_tot_events", "n_events", "median", "hr", "ci"),
groups_lists = list(),
label_all = "All Patients",
label_all = lifecycle::deprecated(),
time_unit = NULL,
na_str = default_na_str()) {
if (lifecycle::is_present(label_all)) {
lifecycle::deprecate_warn(
"0.9.5", "tabulate_survival_subgroups(label_all)",
details =
"Please assign the `label_all` parameter within the `extract_survival_subgroups()` function when creating `df`."
)
}

conf_level <- df$hr$conf_level[1]
method <- df$hr$pval_label[1]

extra_args <- list(groups_lists = groups_lists, conf_level = conf_level, method = method, label_all = label_all)
extra_args <- list(groups_lists = groups_lists, conf_level = conf_level, method = method)

afun_lst <- a_survival_subgroups(na_str = na_str)
colvars <- d_survival_subgroups_colvars(
Expand Down
6 changes: 4 additions & 2 deletions man/survival_biomarkers_subgroups.Rd
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9 changes: 5 additions & 4 deletions man/survival_duration_subgroups.Rd
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26 changes: 26 additions & 0 deletions tests/testthat/_snaps/survival_biomarkers_subgroups.md
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Original file line number Diff line number Diff line change
Expand Up @@ -148,3 +148,29 @@
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239

# label_all argument to extract_survival_subgroups works as expected

Code
res
Output
Total n Total Events Median (DAYS) Hazard Ratio 95% Wald CI p-value (Wald)
——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Age
Full Analysis Set 200 141 753.5 1.01 (0.99, 1.04) 0.3432
Sex
F 110 79 685.2 1.00 (0.96, 1.03) 0.8808
M 90 62 888.5 1.02 (0.99, 1.05) 0.1974
Continuous Level Biomarker 2
LOW 70 52 735.5 1.01 (0.97, 1.06) 0.5584
MEDIUM 68 42 859.0 1.03 (0.98, 1.09) 0.2532
HIGH 62 47 727.8 1.00 (0.96, 1.03) 0.8292
Continuous Level Biomarker 1
Full Analysis Set 200 141 753.5 1.00 (0.95, 1.05) 0.9590
Sex
F 110 79 685.2 1.01 (0.96, 1.07) 0.6215
M 90 62 888.5 0.98 (0.90, 1.07) 0.6939
Continuous Level Biomarker 2
LOW 70 52 735.5 1.00 (0.92, 1.08) 0.9833
MEDIUM 68 42 859.0 0.97 (0.89, 1.06) 0.5218
HIGH 62 47 727.8 1.06 (0.96, 1.17) 0.2239

17 changes: 17 additions & 0 deletions tests/testthat/_snaps/survival_duration_subgroups.md
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Expand Up @@ -223,3 +223,20 @@
MEDIUM 31 14 731.8 17 964.2 <No data> (0.36, 1.61)
HIGH 34 22 654.8 12 1016.3 0.67 (0.33, 1.36)

# label_all argument to extract_survival_subgroups works as expected

Code
res
Output
B: Placebo A: Drug X
Baseline Risk Factors Total Events Events Median (DAYS) Events Median (DAYS) Hazard Ratio 95% Wald CI
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Full Analysis Set 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)

25 changes: 25 additions & 0 deletions tests/testthat/test-survival_biomarkers_subgroups.R
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Original file line number Diff line number Diff line change
Expand Up @@ -152,3 +152,28 @@ testthat::test_that("tabulate_survival_biomarkers na_str argument works as expec
res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
})

testthat::test_that("label_all argument to extract_survival_subgroups works as expected", {
adtte_f <- adtte_local

df <- extract_survival_biomarkers(
variables = list(
tte = "AVAL",
is_event = "is_event",
biomarkers = c("AGE", "BMRKR1"),
subgroups = c("SEX", "BMRKR2")
),
data = adtte_f,
label_all = "Full Analysis Set"
)

lifecycle::expect_deprecated(
result <- tabulate_survival_biomarkers(
df,
time_unit = as.character(adtte_f$AVALU[1]), label_all = "Full Analysis Set"
)
)

res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
})
18 changes: 18 additions & 0 deletions tests/testthat/test-survival_duration_subgroups.R
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Original file line number Diff line number Diff line change
Expand Up @@ -229,3 +229,21 @@ testthat::test_that("tabulate_survival_subgroups na_str argument works as expect
res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
})

testthat::test_that("label_all argument to extract_survival_subgroups works as expected", {
adtte <- adtte_local

df <- extract_survival_subgroups(
variables = list(tte = "AVAL", is_event = "is_event", arm = "ARM", subgroups = c("SEX", "BMRKR2")),
data = adtte,
label_all = "Full Analysis Set"
)

lifecycle::expect_deprecated(
result <- basic_table() %>%
tabulate_survival_subgroups(df, time_unit = adtte$AVALU[1], label_all = "Full Analysis Set")
)

res <- testthat::expect_silent(result)
testthat::expect_snapshot(res)
})
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