docs: documentation simplification

R/argument_convention.R

@@ -203,6 +203,14 @@ NULL
 #'   value indicating worst grade.
 #' @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.
+#' @param decorators `r lifecycle::badge("experimental")`
+#' " (`list` of `teal_transform_module`, named `list` of `teal_transform_module` or" `NULL`) optional,
+#' if not `NULL`, decorator for tables or plots included in the module.
+#' When a named list of `teal_transform_module`, the decorators are applied to the respective output objects.
+#'
+#' Otherwise, the decorators are applied to all objects, which is equivalent as using the name `default`.
+#'
+#' See section "Decorating Module" below for more details.
 #'
 #' @return a `teal_module` object.
 #'

R/tm_a_gee.R

@@ -131,11 +131,10 @@ template_a_gee <- function(output_table,
 #' @inheritParams module_arguments
 #' @inheritParams template_arguments
 #' @inheritParams template_a_gee
-#' @param decorators `r roxygen_decorators_param("tm_a_gee")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_a_gee`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)

R/tm_g_barchart_simple.R

@@ -12,11 +12,10 @@
 #' @param x_facet (`data_extract_spec`)\cr row-wise faceting groups.
 #' @param y_facet (`data_extract_spec`)\cr column-wise faceting groups.
 #' @param plot_options (`list`)\cr list of plot options.
-#' @param decorators `r roxygen_decorators_param("tm_g_barchart_simple")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_barchart_simple`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_ci.R

@@ -185,11 +185,10 @@ template_g_ci <- function(dataname,
 #' @inheritParams module_arguments
 #' @inheritParams template_g_ci
 #' @param color (`data_extract_spec`)\cr the group variable used to determine the plot colors, shapes, and line types.
-#' @param decorators `r roxygen_decorators_param("tm_g_ci")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_ci`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_forest_rsp.R

@@ -240,11 +240,10 @@ template_forest_rsp <- function(dataname = "ANL",
 #' @inheritParams tern::g_forest
 #' @inheritParams module_arguments
 #' @inheritParams template_forest_rsp
-#' @param decorators `r roxygen_decorators_param("tm_g_forest_rsp")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_forest_tte`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`gg`)

R/tm_g_forest_tte.R

@@ -240,11 +240,10 @@ template_forest_tte <- function(dataname = "ANL",
 #' @inheritParams tern::g_forest
 #' @inheritParams module_arguments
 #' @inheritParams template_forest_tte
-#' @param decorators `r roxygen_decorators_param("tm_g_forest_tte")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_forest_tte`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_ipp.R

@@ -176,11 +176,10 @@ template_g_ipp <- function(dataname = "ANL",
 #' @inheritParams template_g_ipp
 #' @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.
-#' @param decorators `r roxygen_decorators_param("tm_g_ipp")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_ipp`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_km.R

@@ -267,11 +267,10 @@ template_g_km <- function(dataname = "ANL",
 #' @inheritParams template_g_km
 #' @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.
-#' @param decorators `r roxygen_decorators_param("tm_g_km")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_km`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_lineplot.R

@@ -211,11 +211,10 @@ template_g_lineplot <- function(dataname = "ANL",
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_g_lineplot
-#' @param decorators `r roxygen_decorators_param("tm_g_lineplot")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_g_lineplot`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_g_pp_patient_timeline.R

@@ -16,14 +16,6 @@
 #'
 #' @inherit template_arguments return
 #'
-#' @section Decorating `tm_g_pp_patient_timeline`:
-#'
-#' This module generates the following objects, which can be modified in place using decorators::
-#' - `plot` (`ggplot2`)
-#'
-#' For additional details and examples of decorators, refer to the vignette
-#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
-#'
 #' @seealso [tm_g_pp_patient_timeline()]
 #'
 #' @keywords internal
@@ -352,10 +344,18 @@ template_patient_timeline <- function(dataname = "ANL",
 #'   all available choices and preselected option for the `CMASTDTM` variable from `dataname_adcm`.
 #' @param dstime_end ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `CMAENDTM` variable from `dataname_adcm`.
-#' @param decorators `r roxygen_decorators_param("tm_")`
 #'
 #' @inherit module_arguments return
 #'
+#' @section Decorating Module:
+#'
+#' This module generates the following objects, which can be modified in place using decorators:
+#' - `plot` (`ggplot2`)
+#'
+#' For additional details and examples of decorators, refer to the vignette
+#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#'
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE

R/tm_g_pp_therapy.R

@@ -241,11 +241,10 @@ template_therapy <- function(dataname = "ANL",
 #'   available choices and preselected option for the `CMDOSFRQ` variable from `dataname`.
 #' @param cmendy ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the `CMENDY` variable from `dataname`.
-#' @param decorators `r roxygen_decorators_param("tm_g_pp_therapy")`
 #'
 #' @inherit module_arguments return
 #'
-#' @section Decorating `tm_g_pp_therapy`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators::
 #' - `plot` (`ggplot2`)

R/tm_g_pp_vitals.R

@@ -206,12 +206,10 @@ template_vitals <- function(dataname = "ANL",
 #' @inheritParams template_vitals
 #' @param xaxis ([teal.transform::choices_selected()])\cr object with all
 #'   available choices and preselected option for the time variable from `dataname` to be put on the plot x-axis.
-#' @param decorators `r roxygen_decorators_param("tm_g_pp_vitals")`
 #'
 #' @inherit module_arguments return
 #'
-#'
-#' @section Decorating `tm_g_pp_vitals`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)

R/tm_t_abnormality.R

@@ -233,11 +233,10 @@ template_abnormality <- function(parentname,
 #' @param baseline_var ([teal.transform::choices_selected()])\cr
 #'   variable for baseline abnormality grade.
 #' @param na_level (`character`)\cr the NA level in the input dataset, default to `"<Missing>"`.
-#' @param decorators `r roxygen_decorators_param("tm_t_abnormality")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_abnormality`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)

R/tm_t_abnormality_by_worst_grade.R

@@ -245,11 +245,10 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint: object_len
 #' object with all available choices and preselected option for variable names that can be used as Worst Low Grade flag.
 #' @param worst_flag_indicator ([teal.transform::choices_selected()])\cr
 #' value indicating worst grade.
-#' @param decorators `r roxygen_decorators_param("tm_t_abnormality_by_worst_grade")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_abnormality_by_worst_grade`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)

R/tm_t_ancova.R

@@ -421,11 +421,10 @@ template_ancova <- function(dataname = "ANL",
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_ancova
-#' @param decorators `r roxygen_decorators_param("tm_t_ancova")`
 #'
 #' @inherit module_arguments return
 #'
-#' @section Decorating `tm_t_ancova`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)

R/tm_t_binary_outcome.R

@@ -347,11 +347,10 @@ template_binary_outcome <- function(dataname,
 #'   `"Not Evaluable (NE)"`, or `"Missing or unevaluable"`, 95% confidence interval will not be calculated.
 #'
 #' * Reference arms are automatically combined if multiple arms selected as reference group.
-#' @param decorators `r roxygen_decorators_param("tm_t_binary_outcome")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_binary_outcome`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` - output of `rtables::build_table`)

R/tm_t_coxreg.R

@@ -336,7 +336,6 @@ template_coxreg_m <- function(dataname,
 #' @inheritParams template_coxreg_m
 #' @param multivariate (`logical`)\cr if `FALSE`, the univariable approach is used instead of the
 #'   multi-variable model.
-#' @param decorators `r roxygen_decorators_param("tm_t_coxreg")`
 #'
 #' @details
 #' The Cox Proportional Hazards (PH) model is the most commonly used method to
@@ -361,7 +360,7 @@ template_coxreg_m <- function(dataname,
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_coxreg`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)
@@ -1102,7 +1101,8 @@ srv_t_coxreg <- function(id,
 
     # Outputs to render.
     table_r <- reactive({
-      decorated_table_q()[["table"]]})
+      decorated_table_q()[["table"]]
+    })
 
     teal.widgets::table_with_settings_srv(
       id = "table",

R/tm_t_events.R

@@ -458,11 +458,10 @@ template_events <- function(dataname,
 #'   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 decorators `r roxygen_decorators_param("tm_t_events")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_events`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)

R/tm_t_events_patyear.R

@@ -189,11 +189,10 @@ template_events_patyear <- function(dataname,
 #'   second variable will be nested under the first variable.
 #' @param events_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for the variable with all event counts.
-#' @param decorators `r roxygen_decorators_param("tm_t_events_patyear")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @section Decorating `tm_t_events_patyear`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)

R/tm_t_events_summary.R

@@ -522,10 +522,7 @@ template_events_summary <- function(anl_name,
 #'
 #' @inherit module_arguments return seealso
 #'
-#' @param decorators `r roxygen_decorators_param("tm_t_events_summary")`
-#'
-#'
-#' @section Decorating `tm_t_events_summary`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` as created from `rtables::build_table`)

R/tm_t_mult_events.R

@@ -279,11 +279,10 @@ template_mult_events <- function(dataname,
 #' @param seq_var ([teal.transform::choices_selected()])\cr object with
 #'   all available choices and preselected option for variable names that can be used as analysis sequence number
 #'   variable. Used for counting the unique number of events.
-#' @param decorators `r roxygen_decorators_param("tm_t_mult_events")`
 #'
 #' @inherit module_arguments return seealso
 #'
-#' #' @section Decorating `tm_t_mult_events`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` - output of `rtables::build_table`)

R/tm_t_tte.R

@@ -386,9 +386,8 @@ template_tte <- function(dataname = "ANL",
 #'   pre-selected option for confidence level, each within range of (0, 1).
 #' @param event_desc_var (`character` or [data_extract_spec()])\cr variable name with the event description
 #'   information, optional.
-#' @param decorators `r roxygen_decorators_param("tm_t_tte")`
 #'
-#' @section Decorating `tm_t_tte`:
+#' @section Decorating Module:
 #'
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`TableTree` - output of `rtables::build_table`)