Merge branch 'main' into cran-release-0.9.0

Signed-off-by: Joe Zhu <sha.joe.zhu@gmail.com>

Author: shajoezhu

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: teal.modules.clinical
 Title: 'teal' Modules for Standard Clinical Outputs
 Version: 0.9.0
-Date: 2024-02-21
+Date: 2024-02-22
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),
     person("Jana", "Stoilova", , "jana.stoilova@roche.com", role = "aut"),

NEWS.md

@@ -2,6 +2,7 @@
 
 ### Breaking Changes
 * Adapted all modules to use `teal_data` objects.
+* Module arguments that previously accepted inputs from `teal.transform::choices_selected()` or `teal.transform::data_extract_spec()` now only accept input from `teal.transform::choices_selected()`. The affected modules are: `tm_a_gee`, `tm_a_mmrm`, `tm_g_ci`, `tm_g_forest_rsp`, `tm_g_forest_tte`, `tm_g_ipp`, `tm_g_km`, `tm_g_lineplot`, `tm_g_pp_adverse_events`, `tm_g_pp_patient_timeline`, `tm_g_pp_therapy`, `tm_g_pp_vitals`, `tm_t_abnormality`, `tm_t_abnormality_by_worst_grade`, `tm_t_ancova`, `tm_t_binary_outcome`, `tm_t_coxreg`, `tm_t_events`, `tm_t_events_by_grade`, `tm_t_events_patyear`, `tm_t_events_summary`, `tm_t_exposure`, `tm_t_logistic`, `tm_t_mult_events`, `tm_t_pp_basic_info`, `tm_t_pp_laboratory`, `tm_t_pp_medical_history`, `tm_t_pp_prior_medication`, `tm_t_shift_by_arm`, `tm_t_shift_by_arm_by_worst`, `tm_t_shift_by_grade`, `tm_t_smq`, `tm_t_summary`, `tm_t_summary_by`, and `tm_t_tte`
 
 ### Enhancements
 * Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.

R/argument_convention.R

@@ -120,34 +120,34 @@ NULL
 #'   with delayed [teal.transform::variable_choices()] or delayed [teal.transform::value_choices()]
 #'   with the elements named `ref` and `comp` that the defined the default
 #'   reference and comparison arms when the arm variable is changed.
-#' @param arm_var ([`teal.transform::choices_selected()`] or [`teal.transform::data_extract_spec()`])\cr object with all
+#' @param arm_var ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for variable names that can be used as `arm_var`.
 #'   It defines the grouping variable(s) in the results table.
 #'   If there are two elements selected for `arm_var`,
 #'   second variable will be nested under the first variable.
-#' @param atirel ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param atirel ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `ATIREL` variable from `dataname`.
-#' @param aval_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param aval_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and pre-selected option for the analysis variable.
-#' @param avalu_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param avalu_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for the analysis unit variable.
-#' @param avisit ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr value of analysis
+#' @param avisit ([teal.transform::choices_selected()])\cr value of analysis
 #'   visit `AVISIT` of interest.
-#' @param baseline_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param baseline_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable values that can be used as `baseline_var`.
-#' @param by_vars ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param by_vars ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for variable names used to split the summary by rows.
-#' @param cmdecod ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param cmdecod ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `CMDECOD` variable from `dataname`.
-#' @param cmindc ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param cmindc ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `CMINDC` variable from `dataname`.
-#' @param cmstdy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param cmstdy ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `CMSTDY` variable from `dataname`.
-#' @param cnsr_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param cnsr_var ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the censoring variable.
-#' @param conf_level ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param conf_level ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and pre-selected option for the confidence level, each within range of (0, 1).
-#' @param cov_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param cov_var ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the covariates variables.
 #' @param dataname (`character`)\cr analysis data used in teal module.
 #' @param default_responses (`list` or `character`)\cr defines
@@ -159,19 +159,19 @@ NULL
 #' @param fixed_symbol_size (`logical`)\cr When (`TRUE`), the same symbol size is used for plotting each estimate.
 #'   Otherwise, the symbol size will be proportional to the sample size in each each subgroup.
 #' @param font_size (`numeric`)\cr numeric vector of length 3 of current, minimum and maximum font size values.
-#' @param hlt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr name of the variable
+#' @param hlt ([teal.transform::choices_selected()])\cr name of the variable
 #'   with high level term for events.
-#' @param id_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object specifying
+#' @param id_var ([teal.transform::choices_selected()])\cr object specifying
 #'   the variable name for subject id.
 #' @param interact_var (`character`)\cr name of the variable that should have interactions
 #'   with arm. If the interaction is not needed, the default option is `NULL`.
 #' @param interact_y (`character`)\cr a selected item from the interact_var column which will be used
 #'   to select the specific `ANCOVA` results when interact_var is discrete. If the interaction is not
 #'   needed, the default option is `FALSE`.
 #' @param label (`character`)\cr menu item label of the module in the teal app.
-#' @param llt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr name of the variable
+#' @param llt ([teal.transform::choices_selected()])\cr name of the variable
 #'   with low level term for events.
-#' @param paramcd ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#' @param paramcd ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the parameter code variable from `dataname`.
 #' @param parentname (`character`)\cr parent analysis data used in teal module, usually this refers to `ADSL`.
 #' @param patient_col (`character`)\cr name of patient ID variable.
@@ -183,27 +183,27 @@ NULL
 #'   For example the [shiny::helpText()] elements are useful.
 #' @param pre_output optional, (`shiny.tag`)\cr with text placed before the output to put the output into context.
 #'   For example a title.
-#' @param strata_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr names of
+#' @param strata_var ([teal.transform::choices_selected()])\cr names of
 #'   the variables for stratified analysis.
-#' @param summarize_vars ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr names of
+#' @param summarize_vars ([teal.transform::choices_selected()])\cr names of
 #'   the variables that should be summarized.
-#' @param subgroup_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param subgroup_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable names that can be used as the default subgroups.
 #' @param time_points ([teal.transform::choices_selected()])\cr object with all available choices and preselected option
 #'   for time points that can be used in [tern::surv_timepoint()].
-#' @param time_unit_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object
+#' @param time_unit_var ([teal.transform::choices_selected()])\cr object
 #'   with all available choices and pre-selected option for the time unit variable.
-#' @param treatment_flag ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr value
+#' @param treatment_flag ([teal.transform::choices_selected()])\cr value
 #'   indicating on treatment records in `treatment_flag_var`.
-#' @param treatment_flag_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr on
+#' @param treatment_flag_var ([teal.transform::choices_selected()])\cr on
 #'   treatment flag variable.
 #' @param useNA (`character`)\cr whether missing data (`NA`) should be displayed as a level.
-#' @param visit_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param visit_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable names that can be used as `visit` variable.
 #'   Must be a factor in `dataname`.
-#' @param worst_flag_indicator ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
+#' @param worst_flag_indicator ([teal.transform::choices_selected()])\cr
 #'   value indicating worst grade.
-#' @param worst_flag_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object
+#' @param worst_flag_var ([teal.transform::choices_selected()])\cr object
 #'   with all available choices and preselected option for variable names that can be used as worst flag variable.
 #'
 #' @return a `teal_module` object.

R/tm_a_gee.R

@@ -205,6 +205,12 @@ tm_a_gee <- function(label,
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(id_var, "choices_selected")
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(visit_var, "choices_selected")
+  checkmate::assert_class(cov_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)

R/tm_a_mmrm.R

@@ -445,7 +445,7 @@ template_mmrm_plots <- function(fit_name,
 #' @inheritParams module_arguments
 #' @inheritParams template_mmrm_tables
 #' @inheritParams template_mmrm_plots
-#' @param method ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param method ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and pre-selected option for the adjustment method.
 #' @param ggplot2_args (`ggplot2_args`) \cr optional, object created by [`teal.widgets::ggplot2_args()`]
 #'   with settings for all the plots or named list of `ggplot2_args` objects for plot-specific settings.
@@ -544,6 +544,12 @@ tm_a_mmrm <- function(label,
   checkmate::assert_string(label)
   checkmate::assert_string(total_label)
   checkmate::assert_string(dataname)
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(id_var, "choices_selected")
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(visit_var, "choices_selected")
+  checkmate::assert_class(cov_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
   checkmate::assert_class(method, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)

R/tm_g_forest_rsp.R

@@ -311,6 +311,11 @@ tm_g_forest_rsp <- function(label,
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)
   checkmate::assert_flag(fixed_symbol_size)
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(subgroup_var, "choices_selected")
+  checkmate::assert_class(strata_var, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
   checkmate::assert_multi_class(default_responses, c("list", "character", "numeric"), null.ok = TRUE)
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)

R/tm_g_forest_tte.R

@@ -300,7 +300,14 @@ tm_g_forest_tte <- function(label,
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(subgroup_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
+  checkmate::assert_class(strata_var, "choices_selected")
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(cnsr_var, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
+  checkmate::assert_class(time_unit_var, "choices_selected")
   checkmate::assert_flag(fixed_symbol_size)
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")

R/tm_g_ipp.R

@@ -174,7 +174,7 @@ template_g_ipp <- function(dataname = "ANL",
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_g_ipp
-#' @param arm_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param arm_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable values that can be used as arm variable.
 #'
 #' @inherit module_arguments return seealso
@@ -302,6 +302,13 @@ tm_g_ipp <- function(label,
   }
 
   logger::log_info("Initializing tm_g_ipp")
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
+  checkmate::assert_class(id_var, "choices_selected")
+  checkmate::assert_class(visit_var, "choices_selected")
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(avalu_var, "choices_selected")
+  checkmate::assert_class(baseline_var, "choices_selected")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)

R/tm_g_km.R

@@ -237,7 +237,7 @@ template_g_km <- function(dataname = "ANL",
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_g_km
-#' @param facet_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
+#' @param facet_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for names of variable that can be used for plot faceting.
 #'
 #' @inherit module_arguments return seealso
@@ -331,6 +331,13 @@ tm_g_km <- function(label,
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
   checkmate::assert_string(parentname)
+  checkmate::assert_class(arm_var, "choices_selected")
+  checkmate::assert_class(paramcd, "choices_selected")
+  checkmate::assert_class(strata_var, "choices_selected")
+  checkmate::assert_class(facet_var, "choices_selected")
+  checkmate::assert_class(time_unit_var, "choices_selected")
+  checkmate::assert_class(aval_var, "choices_selected")
+  checkmate::assert_class(cnsr_var, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")

R/tm_g_lineplot.R

@@ -294,6 +294,7 @@ tm_g_lineplot <- function(label,
   checkmate::assert_string(mid)
   checkmate::assert_string(interval, null.ok = TRUE)
   whiskers <- match.arg(whiskers)
+  checkmate::assert_class(paramcd, "choices_selected")
   checkmate::assert_class(conf_level, "choices_selected")
   checkmate::assert_numeric(plot_height, len = 3, any.missing = FALSE, finite = TRUE)
   checkmate::assert_numeric(plot_height[1], lower = plot_height[2], upper = plot_height[3], .var.name = "plot_height")