Clean up documentation for tm_g_ipp (#1034)

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Fixes #945

---------

Co-authored-by: Davide Garolini <davide.garolini@roche.com>

Author: edelarua

R/argument_convention.R

@@ -17,6 +17,7 @@
 #' @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.
 #' @param aval_var (`character`)\cr name of the analysis value variable.
+#' @param baseline_var (`character`)\cr name of the variable for baseline values of the analysis variable.
 #' @param base_var `r lifecycle::badge("deprecated")` Please use the `baseline_var` argument instead.
 #' @param basic_table_args optional, (`basic_table_args`)\cr object created by [teal.widgets::basic_table_args()]
 #'   with settings for the module table. The argument is merged with option `teal.basic_table_args` and with default

R/tm_g_ipp.R

@@ -1,26 +1,30 @@
 #' Template: Individual Patient Plots
 #'
+#' Creates a valid expression to generate [ggplot2::ggplot()] plots of individual patients.
+#'
 #' @inheritParams template_arguments
-#' @param avalu_var (`string`)\cr variable name designating the unit of the analysis variable.
-#' @param baseline_var (`string`)\cr variable name designating the baseline values of analysis variable.
-#' @param visit_var (`string`)\cr variable name designating the visit timepoint variable.
-#' @param add_baseline_hline (`flag`)\cr adds horizontal line at baseline y-value on plot
-#' @param separate_by_obs (`flag`)\cr creates multi panel plots when TRUE
-#' @param suppress_legend (`flag`)\cr allow user to suppress legend
-#' @param arm_levels (`character`)\cr vector of all arm variable levels.
-#' @param avalu_first (`string`)\cr `avalu` value.
-#' @param paramcd_first (`string`)\cr `paramcd` value.
-#' @param add_avalu (`flag`)\cr allow user to not display value unit in the plot.
-#' @param ggplot2_args optional, (`ggplot2_args`)\cr
-#' object created by [teal.widgets::ggplot2_args()] with settings for the module plot.
-#' For this module, this argument will only accept `ggplot2_args` object with `labs` list of following child elements:
-#' `title`, `subtitle`, `x`, `y`.
-#' No other elements would be taken into account. The argument is merged with option `teal.ggplot2_args` and
-#' with default module arguments (hard coded in the module body).
+#' @param visit_var (`character`)\cr name of the variable for visit timepoints.
+#' @param add_baseline_hline (`logical`)\cr whether a horizontal line should be added to the plot at baseline y-value.
+#' @param separate_by_obs (`logical`)\cr whether to create multi-panel plots.
+#' @param suppress_legend (`logical`)\cr whether to suppress the plot legend.
+#' @param arm_levels (`character`)\cr vector of all levels of `arm_var`.
+#' @param avalu_first (`character`)\cr `avalu_var` text to append to the plot title and y-axis label if `add_avalu` is
+#'   `TRUE`.
+#' @param paramcd_first (`character`)\cr `paramcd` text to append to the plot title and y-axis label.
+#' @param add_avalu (`logical`)\cr whether `avalu_first` text should be appended to the plot title and y-axis label.
+#' @param ggplot2_args optional, (`ggplot2_args`)\cr object created by [teal.widgets::ggplot2_args()] with settings
+#'   for the module plot. For this module, this argument will only accept `ggplot2_args` object with `labs` list of
+#'   the following child elements: `title`, `subtitle`, `x`, `y`. No other elements are taken into account. The
+#'   argument is merged with option `teal.ggplot2_args` and with default module arguments (hard coded in the module
+#'   body).
 #'
-#' For more details, see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.
-#' @keywords internal
+#'   For more details, see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.
+#'
+#' @inherit template_arguments return
 #'
+#' @seealso [tm_g_ipp()]
+#'
+#' @keywords internal
 template_g_ipp <- function(dataname = "ANL",
                            paramcd,
                            arm_var,
@@ -93,8 +97,6 @@ template_g_ipp <- function(dataname = "ANL",
     )
   )
 
-
-
   graph_list <- list()
   graph_list <- add_expr(
     graph_list,
@@ -167,27 +169,20 @@ template_g_ipp <- function(dataname = "ANL",
   y
 }
 
-#' Teal Module: Individual Patient Plot
+#' teal Module: Individual Patient Plots
 #'
-#' This teal module produces grid style Individual patient plot(s) that show
-#' trends in parameter values over time for each patient using data with
-#' `ADaM` structure.
+#' This module produces [ggplot2::ggplot()] type individual patient plots that display trends in parameter
+#' values over time for each patient, using data with ADaM structure.
 #'
 #' @inheritParams module_arguments
 #' @inheritParams template_g_ipp
-#' @param arm_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 `arm_var`.
-#' @param ggplot2_args optional, (`ggplot2_args`)\cr
-#' object created by [teal.widgets::ggplot2_args()] with settings for the module plot.
-#' For this module, this argument will only accept `ggplot2_args` object with `labs` list of following child elements:
-#' `title`, `subtitle`, `x`, `y`.
-#' No other elements would be taken into account. The argument is merged with option `teal.ggplot2_args` and
-#' with default module arguments (hard coded in the module body).
+#' @param arm_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 arm variable.
 #'
-#' For more details, see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`.
+#' @inherit module_arguments return
 #'
-#' @export
+#' @seealso The [TLG Catalog](https://insightsengineering.github.io/tlg-catalog/stable/) where additional example
+#'   apps implementing this module can be found.
 #'
 #' @examples
 #' library(nestcolor)
@@ -254,6 +249,7 @@ template_g_ipp <- function(dataname = "ANL",
 #'   shinyApp(ui = app$ui, server = app$server)
 #' }
 #'
+#' @export
 tm_g_ipp <- function(label,
                      dataname,
                      parentname = ifelse(
@@ -358,7 +354,7 @@ tm_g_ipp <- function(label,
   )
 }
 
-
+#' @keywords internal
 ui_g_ipp <- function(id, ...) {
   a <- list(...) # module args
   is_single_dataset_value <- teal.transform::is_single_dataset(
@@ -460,6 +456,7 @@ ui_g_ipp <- function(id, ...) {
   )
 }
 
+#' @keywords internal
 srv_g_ipp <- function(id,
                       data,
                       reporter,