pre-release other utils functions document update

R/data.R

@@ -1,64 +1,39 @@
 #' Random adverse events
-#'
-#' @description Random adverse events
 #' @docType data
-#'
 #' @usage rADAE
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADAE
 "rADAE"
 
 #' Random lab analysis
-#'
-#' @description Random lab analysis
 #' @docType data
-#'
 #' @usage rADLB
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADLB
 "rADLB"
 
 #' Random response
-#'
-#' @description Random response
 #' @docType data
-#'
 #' @usage rADRS
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADRS
 "rADRS"
 
 #' Random patient listing
-#'
-#' @description Random patient listing
 #' @docType data
-#'
 #' @usage rADSL
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADSL
 "rADSL"
 
-#' Random Time to Event Analysis Dataset
-#'
-#' @description Random Time to Event Analysis Dataset
+#' Random time to event analysis dataset
 #' @docType data
-#'
 #' @usage rADTTE
-#'
 #' @keywords datasets internal
-#'
 #' @source internal
 #' @name rADTTE
 "rADTTE"

R/teal.modules.general.R

@@ -1,4 +1,4 @@
-#' teal.modules.general: General modules to add to a teal application
+#' `teal.modules.general`: General modules to add to a teal application
 #'
 #' The modules in this package are generic modules that should work with any data set
 #' (not necessarily for clinical trials data).

R/utils.R

@@ -1,61 +1,59 @@
-#' Shared Parameters
+#' Shared parameters documentation
 #'
-#' @description Contains arguments that are shared between multiple functions
-#'   in the package to avoid repetition using `inheritParams`.
+#' Defines common arguments shared across multiple functions in the package
+#' to avoid repetition by using `inheritParams`.
 #'
-#' @param plot_height optional, (`numeric`) A vector of length three with `c(value, min and max)`
-#'   for a slider encoding the plot height.
-#' @param plot_width optional, (`numeric`) A vector of length three with `c(value, min and max)`
-#'   for a slider encoding the plot width.
+#' @param plot_height optional, (`numeric`) Specifies the plot height as a three-element vector of
+#' `value`, `min`, and `max` intended for use with a slider UI element.
+#' @param plot_width optional, (`numeric`) Specifies the plot width as a three-element vector of
+#' `value`, `min`, and `max` for a slider encoding the plot width.
 #' @param rotate_xaxis_labels optional, (`logical`) Whether to rotate plot X axis labels. Does not
-#'   rotate by default (`FALSE`).
+#' rotate by default (`FALSE`).
 #' @param ggtheme optional, (`character`) `ggplot2` theme to be used by default. Defaults to `"gray"`.
 #' @param ggplot2_args (`ggplot2_args`) object created by [teal.widgets::ggplot2_args()]
-#'  with settings for the module plot.
-#'  The argument is merged with options variable `teal.ggplot2_args` and default module setup.
+#' with settings for the module plot.
+#' The argument is merged with options variable `teal.ggplot2_args` and default module setup.
 #'
-#'  For more details see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`
+#' For more details see the vignette: `vignette("custom-ggplot2-arguments", package = "teal.widgets")`
 #' @param basic_table_args (`basic_table_args`) object created by [teal.widgets::basic_table_args()]
-#'  with settings for the module table.
-#'  The argument is merged with options variable `teal.basic_table_args` and default module setup.
+#' with settings for the module table.
+#' The argument is merged with options variable `teal.basic_table_args` and default module setup.
 #'
-#'  For more details see the vignette: `vignette("custom-basic-table-arguments", package = "teal.widgets")`
-#' @param pre_output (`shiny.tag`, optional)\cr
+#' For more details see the vignette: `vignette("custom-basic-table-arguments", package = "teal.widgets")`
+#' @param pre_output (`shiny.tag`, optional) Text or UI element to be displayed before the module's output,
+#' providing context or a title.
 #'  with text placed before the output to put the output into context. For example a title.
-#' @param post_output (`shiny.tag`, optional) with text placed after the output to put the output
-#' into context. For example the [shiny::helpText()] elements are useful.
+#' @param post_output (`shiny.tag`, optional) Text or UI element to be displayed after the module's output,
+#' adding context or further instructions. Elements like `shiny::helpText()` are useful.
 #'
 #' @return Object of class `teal_module` to be used in `teal` applications.
 #'
 #' @name shared_params
 #' @keywords internal
 NULL
 
-#' Add axis labels that show facetting variable
+#' Add labels for facets to a ggplot2 object
 #'
-#' Add axis labels that show facetting variable
+#' Enhances a ggplot2 plot by adding labels that describe
+#' the faceting variables along the x and y axes.
 #'
-#' @param p `ggplot2` object to add facet labels to
-#' @param xfacet_label label of facet along x axis (nothing created if NULL),
-#'   if vector, will be concatenated with " & "
-#' @param yfacet_label label of facet along y axis (nothing created if NULL),
-#'   if vector, will be concatenated with " & "
+#' @param p (`ggplot2`) object to which facet labels will be added.
+#' @param xfacet_label (`character`) Label for the facet along the x-axis.
+#' If `NULL`, no label is added. If a vector, labels are joined with " & ".
+#' @param yfacet_label (`character`) Label for the facet along the y-axis.
+#' Similar behavior to `xfacet_label`.
 #'
-#' @return grid grob object (to be drawn with \code{grid.draw})
-#'
-#' @export
+#' @return Returns `grid` or `grob` object (to be drawn with `grid.draw`)
 #'
 #' @examples
-#' # we put donttest to avoid strictr error with seq along.with argument
-#' \donttest{
 #' library(ggplot2)
 #' library(grid)
 #'
 #' p <- ggplot(mtcars) +
 #'   aes(x = mpg, y = disp) +
 #'   geom_point() +
 #'   facet_grid(gear ~ cyl)
-#' p
+#'
 #' xfacet_label <- "cylinders"
 #' yfacet_label <- "gear"
 #' res <- add_facet_labels(p, xfacet_label, yfacet_label)
@@ -68,7 +66,8 @@ NULL
 #' grid.draw(add_facet_labels(p, xfacet_label, yfacet_label = NULL))
 #' grid.newpage()
 #' grid.draw(add_facet_labels(p, xfacet_label = NULL, yfacet_label = NULL))
-#' }
+#'
+#' @export
 #'
 add_facet_labels <- function(p, xfacet_label = NULL, yfacet_label = NULL) {
   checkmate::assert_class(p, classes = "ggplot")
@@ -122,46 +121,42 @@ add_facet_labels <- function(p, xfacet_label = NULL, yfacet_label = NULL) {
 
 #' Call a function with a character vector for the \code{...} argument
 #'
-#' @param fun (\code{character}) Name of a function where the \code{...} argument
+#' @param fun (`character`) Name of a function where the \code{...} argument
 #'   shall be replaced by values from \code{str_args}.
-#' @param str_args (\code{character}) A character vector that the function shall
+#' @param str_args (`character`) A character vector that the function shall
 #'  be executed with
 #'
-#' @return: call (i.e. expression) of the function provided by \code{fun}
+#' @return Call (i.e. expression) of the function provided by \code{fun}
 #'  with arguments provided by \code{str_args}.
-#' @keywords internal
 #'
 #' @examples
-#' \dontrun{
+#' call_fun_dots <- getFromNamespace("call_fun_dots", "teal.modules.general")
+#'
 #' a <- 1
 #' b <- 2
 #' call_fun_dots("sum", c("a", "b"))
 #' eval(call_fun_dots("sum", c("a", "b")))
-#' }
+#'
+#' @keywords internal
+#'
 call_fun_dots <- function(fun, str_args) {
   do.call("call", c(list(fun), lapply(str_args, as.name)), quote = TRUE)
 }
 
-#' Get variable name with label
+#' Generate a string for a variable including its label
 #'
-#' @param var_names (\code{character}) Name of variable to extract labels from.
-#' @param dataset (\code{dataset}) Name of analysis dataset.
-#' @param prefix (\code{character}) String to paste to the beginning of the
+#' @param var_names (`character`) Name of variable to extract labels from.
+#' @param dataset (`dataset`) Name of analysis dataset.
+#' @param prefix (`character`) String to paste to the beginning of the
 #'   variable name with label.
-#' @param suffix (\code{character}) String to paste to the end of the variable
+#' @param suffix (`character`) String to paste to the end of the variable
 #'   name with label.
-#' @param wrap_width (\code{numeric}) Number of characters to wrap original
+#' @param wrap_width (`numeric`) Number of characters to wrap original
 #'   label to. Defaults to 80.
 #'
-#' @return (\code{character}) String with variable name and label.
+#' @return (`character`) String with variable name and label.
 #' @keywords internal
 #'
-#' @examples
-#' \dontrun{
-#' ADSL <- teal.modules.general::rADSL
-#'
-#' varname_w_label("AGE", ADSL)
-#' }
 varname_w_label <- function(var_names,
                             dataset,
                             wrap_width = 80,
@@ -205,17 +200,20 @@ shape_names <- c(
 #' Get icons to represent variable types in dataset
 #'
 #' @param var_type (`character`)\cr
-#'  of R internal types (classes).
+#'  of `R` internal types (classes).
 #'
-#' @return (`character`)\cr
-#'  vector of HTML icons corresponding to data type in each column.
-#' @keywords internal
+#' @return Vector of HTML icons corresponding to data type in each column.
 #'
 #' @examples
-#' teal.modules.general:::variable_type_icons(c(
+#' variable_type_icons <- getFromNamespace("variable_type_icons", "teal.modules.general")
+#'
+#' variable_type_icons(c(
 #'   "integer", "numeric", "logical", "Date", "POSIXct", "POSIXlt",
 #'   "factor", "character", "unknown", ""
 #' ))
+#'
+#' @keywords internal
+#'
 variable_type_icons <- function(var_type) {
   checkmate::assert_character(var_type, any.missing = FALSE)
 
@@ -256,10 +254,11 @@ variable_type_icons <- function(var_type) {
 #' not work with `devtools`. Therefore, we redefine this method in each package
 #' as needed. Thus, we do not export this method
 #'
-#' @param pattern (`character`) pattern of files to be included
+#' @param pattern (`character`) optional regular expression to match the file names to be included.
 #'
-#' @return HTML code that includes `CSS` files
+#' @return HTML code that includes `CSS` files.
 #' @keywords internal
+#'
 include_css_files <- function(pattern = "*") {
   css_files <- list.files(
     system.file("css", package = "teal.modules.general", mustWork = TRUE),
@@ -271,12 +270,14 @@ include_css_files <- function(pattern = "*") {
   return(shiny::singleton(shiny::tags$head(lapply(css_files, shiny::includeCSS))))
 }
 
-
-#' Get a string with java-script code checking if the specific tab is clicked
-#' @description will be the input for `shiny::conditionalPanel()`
-#' @param id `character(1)` the id of the tab panel with tabs.
-#' @param name `character(1)` the name of the tab.
+#' JavaScript condition to check if a specific tab is active
+#'
+#' @param id (`character(1)`) the id of the tab panel with tabs.
+#' @param name (`character(1)`) the name of the tab.
+#' @return JavaScript expression to be used in `shiny::conditionalPanel()` to determine
+#' if the specified tab is active.
 #' @keywords internal
+#'
 is_tab_active_js <- function(id, name) {
   # supporting the bs3 and higher version at the same time
   sprintf(