update documentation tm_missing_data

Author: kartikeyakirar

R/tm_missing_data.R

@@ -1,21 +1,21 @@
-#' Missing data module
+#' Missing data analysis module
 #'
-#' Present analysis of missing observations and patients.
-#' specifically designed for use with `data.frames`.
+#' Module analyzes missing data in `data.frame`s to help users explore missing observations and
+#' gain insights into the completeness of their data.
+#' It is useful for clinical data analysis within the context of CDISC standards and
+#' adaptable for general data analysis purposes.
 #'
 #' @inheritParams teal::module
 #' @inheritParams shared_params
-#' @param parent_dataname (`character(1)`) If this `dataname` exists in then "the by subject"graph is displayed.
-#'   For `CDISC` data. In non `CDISC` data this can be ignored. Defaults to `"ADSL"`.
-#' @param ggtheme optional, (`character`) `ggplot2` theme to be used by default. Defaults to `"classic"`.
+#' @param parent_dataname (`character(1)`) Specifies the parent dataset name. Default is `ADSL` for CDISC data.
+#' If provided and exists, enables additional analysis "by subject". For non-CDISC data, this parameter can be ignored.
+#' @param ggtheme (`character`, optional) Specifies the default `ggplot2` theme for plots. Defaults to `classic`.
 #'
 #' @templateVar ggnames "Summary Obs", "Summary Patients", "Combinations Main", "Combinations Hist", "By Subject"
 #' @template ggplot2_args_multi
 #'
-#' @export
-#'
 #' @examples
-#'
+#' library(teal.widgets)
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
@@ -26,22 +26,25 @@
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_missing_data(
+#'   modules = modules(
+#'     tm_missing_data(
 #'       ggplot2_args = list(
-#'         "Combinations Hist" = teal.widgets::ggplot2_args(
+#'         "Combinations Hist" = ggplot2_args(
 #'           labs = list(subtitle = "Plot produced by Missing Data Module", caption = NULL)
 #'         ),
-#'         "Combinations Main" = teal.widgets::ggplot2_args(labs = list(title = NULL))
+#'         "Combinations Main" = ggplot2_args(labs = list(title = NULL))
 #'       )
 #'     )
 #'   )
 #' )
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
 #' }
+#'
+#' @export
+#'
 tm_missing_data <- function(label = "Missing data",
                             plot_height = c(600, 400, 5000),
                             plot_width = NULL,
@@ -89,6 +92,7 @@ tm_missing_data <- function(label = "Missing data",
   )
 }
 
+# UI function for the missing data module.
 ui_page_missing_data <- function(id, pre_output = NULL, post_output = NULL) {
   ns <- NS(id)
   shiny::tagList(
@@ -113,6 +117,7 @@ ui_page_missing_data <- function(id, pre_output = NULL, post_output = NULL) {
   )
 }
 
+# Server function for the missing data module.
 srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_dataname,
                                   plot_height, plot_width, ggplot2_args, ggtheme) {
   moduleServer(id, function(input, output, session) {
@@ -199,6 +204,7 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
   })
 }
 
+# UI function for the missing data module.
 ui_missing_data <- function(id, by_subject_plot = FALSE) {
   ns <- NS(id)
 
@@ -268,6 +274,8 @@ ui_missing_data <- function(id, by_subject_plot = FALSE) {
   )
 }
 
+#' @noRd
+#' @keywords internal
 encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, datanames) {
   ns <- NS(id)
 
@@ -356,6 +364,7 @@ encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, data
   )
 }
 
+# Server function for the missing data module.
 srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, parent_dataname,
                              plot_height, plot_width, ggplot2_args) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
@@ -460,7 +469,7 @@ srv_missing_data <- function(id, data, reporter, filter_panel_api, dataname, par
               } else {
                 labels <- ifelse(cols == new_col_name | cols == "", cols, paste0(column_labels[cols], " [", cols, "]"))
               }
-              return(labels)
+              labels
             },
           env = list(
             new_col_name = new_col_name,