NEWS.md

broom.helpers (development version)

Fixes

• variable labels are now returned by model_list_variables() for svycoxph models (#275)

broom.helpers 1.17.0

Deprecated functions and changes in selectors functions

• selectors such as all_categorical() are now compatible with gtsummary version ≥ 2.0.0 (#270)
• new function scope_tidy() to scope a tidy tibble allowing to tidy select (#270)
• .select_to_varnames(), .formula_list_to_named_list(), .generic_selector() and .is_selector_scoped() are now deprecated and will be removed in a future release: you may consider cards::process_selectors() and cards::process_formula_selectors() as alternatives (#270)

Fixes

• model_get_model_frame.coxph() has been fixed to return a correct model frame a subject identifier is passed to survival::coxph() (#268)

Documentation

• Documentation has been improved, showing now clearly the type expected for each argument (#272)

broom.helpers 1.16.0

New features

• new argument model_matrix_attr in tidy_and_attach() and tidy_plus_plus() to attach model frame and model matrix to the model as attributes for saving some execution time (#254)
• tidy_add_n() now returns n_ind the number of individuals, in addition to the number of observations (#251)
• by default, tidy_parameters() calls now parameters::model_parameters() with pretty_names = FALSE for saving execution time (#259)
• internal code now uses the native R pipe (|>), requiring therefore R >= 4.2 (#262)

Deprecated support

• biglmm::bigglm() not supported anymore as biglmm has been removed from CRAN

Deprecated functions

• tidy_marginal_means() is now deprecated, following deprecation of marginaleffects::marginal_means(). Use instead tidy_marginal_predictions() with the option newdata = "marginalmeans".
• tidy_margins() is now indicated as superseded and may be deprecated if margins is removed from CRAN. tidy_avg_slopes() could be used as an alternative. (#252)

Fixes

• tidy_multgee() has been fixed to properly identify the different y.levels (#260 @jackmwolf)
• tidy_marginal_predictions() has been updated to avoid the use of the deprecated function marginaleffects::datagridcf() (#256)

broom.helpers 1.15.0

New supported models

• support for mmrm::mmrm() models (#228)
• support for survival::cch() models (#242)

New features

• new tidy_post_fun argument in tidy_plus_plus() (#235)

Fix

• fix the order of the levels of categorical variables in the results of tidy_marginal_predictions() (#245)
• fix in supported_models
• bug fix when using tidy_parameters() for mixed models (#238)
• bug fix for survey::svyglm() models with replicate weights (#240)

broom.helpers 1.14.0

New features

• support for MASS::contr.sdif() contrasts (#230)
• support for pscl::zeroinfl() and pscl::hurdle() models (#232)
• support for betareg::betareg() models (#234)

Fix

• input of packageVersion() should be a character string (#225)

broom.helpers 1.13.0

New features

• tidy_add_estimate_to_reference_rows() now also populate p-values and confidence intervals for sum contrasts (#220)
• Marginal tidiers are now compatible with nnet::multinom(), MASS::polr(), ordinal::clm() and ordinal::clmm() models, as long as the type of models is supported by the corresponding package, for example, margins does not currently support nnet::multinom() models (#215)

Improvements

• Marginal predictions vignette has been updated to follow changes in marginaleffects version 0.10.0 (#216)

broom.helpers 1.12.0

New features

• Set of functions to support marginal predictions, contrasts and slopes / effects (#202):
  • A dedicated article presenting the concepts and the different functions has been added to the package documentation website
  • Several tidiers are provided to tidy results in a way that it could be used by broom.helpers functions.
  • Marginal Predictions: tidy_marginal_predictions(), plot_marginal_predictions(), tidy_all_effects(), and tidy_ggpredict()
  • Marginal Means: tidy_marginal_means()
  • Marginal Contrasts: tidy_avg_comparisons() and tidy_marginal_contrasts()
  • Marginal Effects: tidy_avg_slopes() and tidy_margins()
• New method model_list_higher_order_variables() to list the highest order combinations of variables (#202)
• New method model_get_response_variable() to get the name of the response variable (#202)
• New helper function seq_range() to generate a sequence of values between the minimum and the maximum of a vector (#202)
• New argument contrasts_adjust in tidy_plus_plus(), tidy_add_pairwise_contrasts() and model_get_pairwise_contrasts() allowing to change the adjustment method used to compute pairwise contrasts (#204)

broom.helpers 1.11.0

New features

• New functions tidy_add_pairwise_contrasts() and model_get_pairwise_contrasts() to compute pairwise contrasts of categorical variables with emmeans, and corresponding new arguments in tidy_plus_plus() (#192)
• New tidier tidy_margins() to display Average Marginal Effects (#195)
• New tidier tidy_all_effects() to display Marginal Predictions (#195)
• New tidier tidy_ggpredict() to display Conditional Predictions (#195)

Bug fixes and improvements

• Better messages when exponentiate argument is not appropriate (#197)

broom.helpers 1.10.0

New features

• tidy_select_variables() now sorts the variables according to include (#183)

New supported models

• Support for logitr::logitr() models (#179)
• Experimental support for multgee::nomLORgee() and multgee::ordLORgee() models (#185)

Bug fixes and improvements

• Improvement of .get_package_dependencies() to be more efficient. It now looks only at a single package description file (#178)
• New function .get_all_packages_dependencies() to list all dependencies of all packages (#178)
• Bug fix in .get_min_version_required() (#181)

broom.helpers 1.9.0

New features

• New function .get_package_dependencies() listing all dependencies, including minimum version required, of a package. (#171)
• Improvement of .assert_package() now taking into account the comparison operator (> or >=) when a minimum version is required (#171)

Bug fixes and improvements

• Compatibility with upcoming tidyselect v1.2.0 (#173)
• Avoid an unwanted warning for some mgcv::gam() models (#175)

broom.helpers 1.8.0

New supported models

• Support for parsnip::model_fit objects (#161)
• Support for biglm::bigglm() and biglmm::bigglm() models (#155)
• Support for fixest::feglm(), fixest::femlm(), fixest::feols() and fixest::feNmlm() (requires R>=4.1) (#167)

New features

• Support for dplyr::vars() (also exported by {gtsummary}) as a selector has now been deprecated. Users will be warned that support for vars() will eventually be removed from the package (#154)
• .is_selector_scoped(), an internal function used in generating custom selector functions, is now exported (#163)

broom.helpers 1.7.0

New features

• The .assert_package() now uses rlang::check_installed() and rlang::is_installed() to check whether needed packages are installed. The rlang::check_installed() prompts user to install needed package when run interactively. (#147)
• tidy_add_n() and model_get_n() support for tidycmprsk::crr() models (#143)
• Listing of supported models is now available in supported_models tibble (#145)

Bug fixes

• Avoiding duplicating rows when applying tidy_add_n() to a mgcv::gam() model with smooth terms (#150)

broom.helpers 1.6.0

New supported models

• Support for plm::plm() models (#140)

New features

• The .formula_list_to_named_list() now respects the select_single= argument for all inputs types. Previously, named lists were ignored.
• Added new argument .formula_list_to_named_list(null_allowed=) argument that works in conjunction with type_check= asserting the class/type of the RHS of the formula (or the value of the named list) (#137)
• Better error message in .formula_list_to_named_list() (#136)
• Two additional select helpers all_ran_pars() and all_ran_vals()

Bug fixes

• Fix so .formula_list_to_named_list(type_check=) checks RHS of a formula and the value of named list. (#138)

broom.helpers 1.5.0

New features

• New method model_get_coefficients_type.tidycrr() (#128)
• Updated error messaging about using broom.helpers::tidy_parameters() to include the package prefix. This message sometimes appears while running gtsummary::tbl_regression() where some users may not be aware where the tidy_paramters() function lives. (#129)
• .formula_list_to_named_list() improvement: it is now possible to add a type check (#132)
• New functions .assert_package() and .get_min_version_required() to check for a package's installation status and whether the installed version meets the minimum required version from the DESCRIPTION file (#134)

Bug fixes

• Bug fix for identifying the levels of a logical variable (#125)
• Bug fix for nnet::multinom() models with a binary outcome (#130)

broom.helpers 1.4.0

New supported models

• Support for glmmTMB::glmmTMB() models (#119)

New features

• Function arguments that accept formula-list values now have more flexible inputs. (#121)
  • The passed list may now be a combination of named lists and lists of formulas, e.g. list(trt ~ 1, all_continuous() ~ 2).
  • The shortcut ~ <value> may be now used to indicate everything() ~ <value>

Bug fixes

• Bug fix for computing n for some binomial models computed with lme4::glmer() (#116)
• Populating effect column when adding reference rows (#117)

broom.helpers 1.3.0

New supported models

• Support of rstanarm::stan_glm() models
• Basic support for VGAM::vglm() models (#105)

New features

• Custom tieder tidy_parameters() based on parameters::model_parameters() (#104)
• Custom tieder tidy_with_broom_or_parameters() (#104)
• By default, tidy_plus_plus() now uses tidy_with_broom_or_parameters()
• model_get_coefficients_type() now returns "prop_hazard" for cloglog-binomial models (#106)

broom.helpers 1.2.1

Bug fixes

• Better identification of term labels for interaction terms using sum contrasts (#108)
• Now tidy_add_n() works with multinomial models when y is not coded as a factor (#109)
• glue added to Suggests

broom.helpers 1.2.0

New features

• model_get_coefficients_type() now returns "relative_risk" for log-binomial models (#101)
• New function tidy_disambiguate_terms() for disambiguating random-effect terms in mixed models and new options for tidy_plus_plus(): disambiguate_terms (TRUE by default) and disambiguate_sep (#98)
• For mixed models, var_type column is now equal to "ran_pars" or "ran_vals" for random-effect parameters and values, based of the effect column returned by broom.mixed::tidy() (#90)
• New contrasts type ("no.contrast") returned by model_list_contrasts()
• New function tidy_add_n() to add the number of observations (and for relevant models the number of events and exposure time) (#64)
• New option add_n in tidy_plus_plus() (#64)
• New functions model_get_n(), model_get_weights(), model_get_offset(), model_get_response() and model_compute_terms_contributions() (#64)

New supported models

• Support of lfe::felm() models (#79)
• Support of brms::brm() models (#89)
• Basic support of cmprsk::crr() models (#91)
• Basic support of stats::nls() models (#97)
• Models with categorical variable and no intercept now supported (#85)
• Added support for mgcv::gam() models. (#82)

Bug fixes and other changes

• Minor breaking change: strict argument removed from tidy_identify_variables() (#99)
• Replaced usethis::ui_*() messaging with cli::cli_*() (#94)
• Bug fix in tidy_add_term_labels() for variables with non standard names (#77)
• Fix in vignette for old versions of rmarkdown (#95)

broom.helpers 1.1.0

• Minor breaking change: column var_type returned by tidy_identify_variables() is now equal to "dichotomous" for categorical variables with only 2 levels
• Minor breaking changes: for intercepts terms, tidy_identify_variables() now populates variable column by term content, instead of NA (#66)
• Minor breaking change: If the variables can't be identified by tidy_identify_variables(), the variable column is now populated with the content of the term column (#63)
• Exporting select helper utility functions (#65)
  • .generic_selector(): makes it easy to create selecting functions like all_continuous().
  • .select_to_varnames(): converts selecting syntax into character varnames
  • .formula_list_to_named_list(): takes the formula selecting syntax and converts it to a named list.
• New selecting functions all_continuous(), all_categorical(), all_dichotomous(), all_contrasts(), all_intercepts() and all_interaction() for selecting variables from models (#54)
• Added support for multiple imputation models from the {mice} package. The model passed must be the un-pooled models, and the pooling step included in tidy_fun= (#49 @ddsjoberg)
• New function tidy_select_variables() to keep/drop selected variables in the output (#45)
• New functions tidy_add_coefficients_type() and model_get_coefficients_type to get the type of coefficients (generic, logistic, Poisson or proportional hazard) used by a model (#46)
• tidy_add_contrasts() and model_list_contrasts() now return an additional column contrasts_type
• New no_reference_row argument for tidy_add_reference_rows() (#47)
• New method model_get_nlevels to get the number of levels of categorical variables
• New column var_nlevels returned by tidy_identify_variables(), model_identify_variables() and tidy_plus_plus()
• Categorical terms can now be customized with a pattern taking into account term level, reference level and/or variable label, see model_list_terms_levels() and categorical_terms_pattern in tidy_plus_plus() and tidy_add_term_labels (#61)
• model_list_terms_levels() now returns additional columns (level, reference_level, contrasts_type, var_label, var_levels and dichotomous)
• model_list_variables() now returns an additional var_label column
• The exponentiate argument is now passed to the tidy_*() functions, as an attribute attached to the tibble, as well as custom labels (variable_labels and term_labels)
• show_single_row argument now accepts tidyselect notation (#51 @ddsjoberg)
• tidy_add_estimate_to_reference_rows() now relies on emmeans for sum contrasts, allowing to cover a wider range of models
• Tibbles returned by tidy_* functions also inherits of "broom.helpers" class (#56)
• interaction_sep argument has been added to tidy_plus_plus()
• Better management of variables with non standard names (#67)
• .clean_backticks() and .escape_regex() are now exported
• Bug fix for non standard variable names containing a character that would have a special meaning in a regular expression (#44)
• Bug fix in tidy_add_header_rows() for nnet::multinom models: label for header rows was missing (#50)
• Bug fix: now tidy_identify_variables() correctly identify class "integer" for this type of variables (#57)
• Bug fix for tidy_add_header_rows() for continuous variables with a non standard name (#70)

broom.helpers 1.0.0

• Initial version