Clean up documentation for tm_g_pp_therapy

R/argument_convention.R

@@ -12,6 +12,7 @@
 #' @param add_total (`logical`)\cr whether to include column with total number of patients.
 #' @param anl_name (`character`)\cr analysis data used in teal module.
 #' @param arm_var (`character`)\cr variable names that can be used as `arm_var`.
+#' @param atirel (`character`)\cr name of time relation of medication variable.
 #' @param aval `r lifecycle::badge("deprecated")` Please use the `aval_var` argument instead.
 #' @param avalu `r lifecycle::badge("deprecated")` Please use the `avalu_var` argument instead.
 #' @param avalu_var (`character`)\cr name of the analysis value unit variable.
@@ -23,6 +24,9 @@
 #'
 #'   For more details, see the vignette: `vignette("custom-basic-table-arguments", package = "teal.widgets")`.
 #' @param by_vars (`character`)\cr variable names used to split the summary by rows.
+#' @param cmdecod (`character`)\cr name of standardized medication name variable.
+#' @param cmindc (`character`)\cr name of indication variable.
+#' @param cmstdy (`character`)\cr name of study relative day of start of medication variable.
 #' @param cnsr_var (`character`)\cr name of the censoring variable.
 #' @param combine_comp_arms (`logical`)\cr triggers the combination of comparison arms.
 #' @param compare_arm (`logical`)\cr triggers the comparison between study arms.
@@ -37,6 +41,7 @@
 #' @param drop_arm_levels (`logical`)\cr drop the unused `arm_var` levels.
 #'   When `TRUE`, `arm_var` levels are set to those used in the `dataname` dataset. When `FALSE`,
 #'   `arm_var` levels are set to those used in the `parantname` dataset.
+#' @param font_size (`numeric`)\cr font size value.
 #' @param ggplot2_args optional, (`ggplot2_args`)\cr object created by [teal.widgets::ggplot2_args()] with settings
 #'   for the module plot. The argument is merged with option `teal.ggplot2_args` and with default module arguments
 #'   (hard coded in the module body).
@@ -50,6 +55,7 @@
 #' @param interact_y (`character`)\cr a selected item from the interact_var column which will be used to select the
 #'   specific `ANCOVA` results. If the interaction is not needed, the default option is `FALSE`.
 #' @param llt (`character`)\cr name of the variable with low level term for events.
+#' @param patient_id (`character`)\cr patient ID.
 #' @param na_level (`string`)\cr used to replace all `NA` or empty values
 #'   in character or factor variables in the data. Defaults to `"<Missing>"`. To set a
 #'   default `na_level` to apply in all modules, run `set_default_na_str("new_default")`.
@@ -110,13 +116,21 @@ NULL
 #'   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
+#'   available choices and preselected option for the `ATIREL` variable from `dataname`.
 #' @param aval_var (`choices_selected` or `data_extract_spec`)\cr object with all available choices and preselected
 #'   option for the analysis variable.
 #' @param avisit (`choices_selected` or `data_extract_spec`)\cr value of analysis visit `AVISIT` of interest.
 #' @param baseline_var ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with
 #'   all available choices and preselected option for variable values that can be used as `baseline_var`.
 #' @param by_vars (`choices_selected` or `data_extract_spec`)\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
+#'   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
+#'   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
+#'   available choices and preselected option for the `CMSTDY` variable from `dataname`.
 #' @param cnsr_var (`choices_selected` or `data_extract_spec`)\cr object with all available choices and preselected
 #'   option for the censoring variable.
 #' @param conf_level (`choices_selected`)\cr object with all available choices and preselected option for the
@@ -131,6 +145,7 @@ NULL
 #'   values and `levels` of default level choices.
 #' @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 (`choices_selected` or `data_extract_spec`)\cr name of the variable with high level term for events.
 #' @param id_var (`choices_selected` or `data_extract_spec`)\cr object specifying the variable name for subject id.
 #' @param interact_var (`character`)\cr name of the variable that should have interactions
@@ -142,6 +157,7 @@ NULL
 #' @param llt (`choices_selected` or `data_extract_spec`)\cr name of the variable with low level term for events.
 #' @param paramcd (`choices_selected` or `data_extract_spec`)\cr variable value designating the studied parameter.
 #' @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.
 #' @param plot_height optional, (`numeric`)\cr a vector of length three with `c(value, min, max)`. Specifies the
 #'   height of the main plot and renders a slider on the plot to interactively adjust the plot height.
 #' @param plot_width optional, (`numeric`)\cr a vector of length three with `c(value, min, max)`. Specifies the width

R/tm_g_pp_therapy.R

@@ -1,22 +1,21 @@
-#' Template: Therapy
+#' Template: Patient Profile Therapy Table and Plot
 #'
-#' Creates a therapy template call.
+#' Creates a valid expression to generate a patient profile therapy table and [ggplot2::ggplot()] plot using ADaM
+#' datasets.
 #'
 #' @inheritParams template_arguments
-#' @param atirel (`character`)\cr name of time relation of medication variable.
-#' @param cmdecod (`character`)\cr name of standardized medication name variable.
-#' @param cmindc (`character`)\cr name of indication variable.
 #' @param cmdose (`character`)\cr name of dose per administration variable.
 #' @param cmtrt (`character`)\cr name of reported name of drug, med, or therapy variable.
 #' @param cmdosu (`character`)\cr name of dose units variable.
 #' @param cmroute (`character`)\cr name of route of administration variable.
 #' @param cmdosfrq (`character`)\cr name of dosing frequency per interval variable.
-#' @param cmstdy (`character`)\cr name of study day of start of medication variable.
 #' @param cmendy (`character`)\cr name of study day of end of medication variable.
-#' @param patient_id (`character`)\cr patient ID.
-#' @param font_size (`numeric`)\cr numeric vector of length 3 for current, min and max font size values.
-#' @keywords internal
 #'
+#' @inherit template_arguments return
+#'
+#' @seealso [tm_g_pp_therapy()]
+#'
+#' @keywords internal
 template_therapy <- function(dataname = "ANL",
                              atirel = "ATIREL",
                              cmdecod = "CMDECOD",
@@ -230,36 +229,26 @@ template_therapy <- function(dataname = "ANL",
   y
 }
 
-#' Teal Module: Patient Profile Therapy Teal Module
+#' teal Module: Patient Profile Therapy Table and Plot
 #'
-#' This teal module produces a patient profile therapy plot using `ADaM` datasets.
+#' This module produces a patient profile therapy table and [ggplot2::ggplot()] type plot using ADaM datasets.
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_therapy
-#' @param patient_col (`character`)\cr patient ID column to be used.
-#' @param atirel ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `ATIREL` column of the `ADCM` dataset.
-#' @param cmdecod ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDECOD` column of the `ADCM` dataset.
-#' @param cmdose ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSE` column of the `ADCM` dataset.
-#' @param cmtrt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMTRT` column of the `ADCM` dataset.
-#' @param cmdosu ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSU` column of the `ADCM` dataset.
-#' @param cmroute ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMROUTE` column of the `ADCM` dataset.
-#' @param cmdosfrq ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMDOSFRQ` column of the `ADCM` dataset.
-#' @param cmstdy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMSTDY` column of the `ADCM` dataset.
-#' @param cmendy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMENDY` column of the `ADCM` dataset.
-#' @param cmindc ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr
-#' `CMINDC` column of the `ADCM` dataset.
-#' @param font_size (`numeric`)\cr numeric vector of length 3 for current, min and max font size values.
+#' @param cmdose ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSE` variable from `dataname`.
+#' @param cmtrt ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMTRT` variable from `dataname`.
+#' @param cmdosu ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSU` variable from `dataname`.
+#' @param cmroute ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMROUTE` variable from `dataname`.
+#' @param cmdosfrq ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMDOSFRQ` variable from `dataname`.
+#' @param cmendy ([teal.transform::choices_selected()] or [teal.transform::data_extract_spec()])\cr object with all
+#'   available choices and preselected option for the `CMENDY` variable from `dataname`.
 #'
-#' @export
+#' @inherit module_arguments return
 #'
 #' @examples
 #' library(nestcolor)
@@ -339,6 +328,7 @@ template_therapy <- function(dataname = "ANL",
 #'   shinyApp(app$ui, app$server)
 #' }
 #'
+#' @export
 tm_g_pp_therapy <- function(label,
                             dataname = "ADCM",
                             parentname = "ADSL",
@@ -412,6 +402,7 @@ tm_g_pp_therapy <- function(label,
   )
 }
 
+#' @keywords internal
 ui_g_therapy <- function(id, ...) {
   ui_args <- list(...)
   is_single_dataset_value <- teal.transform::is_single_dataset(
@@ -531,7 +522,7 @@ ui_g_therapy <- function(id, ...) {
   )
 }
 
-
+#' @keywords internal
 srv_g_therapy <- function(id,
                           data,
                           reporter,