149 revise documentation

R/get_dt_rows.R

@@ -1,8 +1,9 @@
-#' Maps the `lengthMenu`selected value property of `DT::datatable` to a Shiny variable.
+#' Map `lenghtMenu` property
 #'
-#' @description `r lifecycle::badge("stable")`
-#' @param dt_name \code{ns()} of `inputId` of the `DT::datatable`
-#' @param dt_rows \code{ns()} of `inputId` of the variable that holds the current selected value of `lengthMenu`
+#' @description `r lifecycle::badge("stable")`\cr
+#' Maps the `lengthMenu` selected value property of `DT::datatable` to a `shiny` variable.
+#' @param dt_name `ns()` of `inputId` of the `DT::datatable`
+#' @param dt_rows `ns()` of `inputId` of the variable that holds the current selected value of `lengthMenu`
 #'
 #' @name get_dt_rows
 #'

R/optionalInput.R

@@ -450,7 +450,7 @@ extract_raw_choices <- function(choices, sep) {
 
 #' if min or max are `NA` then the slider widget will be hidden
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description `r lifecycle::badge("stable")`\cr
 #' Hidden input widgets are useful to have the `input[[inputId]]` variable
 #' on available in the server function but no corresponding visual clutter from
 #' input widgets that provide only a single choice.

R/panel_group.R

@@ -1,12 +1,50 @@
 #' Panel group widget
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description `r lifecycle::badge("experimental")`\cr
+#' Designed to group [`panel_item`] elements. Used to handle `shiny` inputs in the encoding panel.
 #' @param id optional, (`character`)\cr
 #' @param ... (`shiny.tag`)\cr
 #'  panels created by [panel_group()]
 #'
 #' @return (`shiny.tag`)
 #'
+#' @examples
+#'
+#' library(shiny)
+#' panel_group(
+#'   panel_item(
+#'     title = "Display",
+#'     collapsed = FALSE,
+#'     checkboxGroupInput(
+#'       "check",
+#'       "Tables display",
+#'       choices = LETTERS[1:3],
+#'       selected = LETTERS[1]
+#'     ),
+#'     radioButtons(
+#'       "radio",
+#'       label = "Plot type",
+#'       choices = letters[1:2],
+#'       selected = letters[1]
+#'     )
+#'   ),
+#'   panel_item(
+#'     title = "Pre-processing",
+#'     radioButtons(
+#'       "filtering",
+#'       "What to filter",
+#'       choices = LETTERS[1:4],
+#'       selected = LETTERS[1]
+#'     ),
+#'     radioButtons(
+#'       "na_action",
+#'       "NA action",
+#'       choices = letters[1:3],
+#'       selected = letters[1]
+#'     )
+#'   )
+#' )
+#'
 #' @export
 panel_group <- function(..., id = NULL) {
   checkmate::assert_string(id, null.ok = TRUE)
@@ -35,9 +73,9 @@ panel_group <- function(..., id = NULL) {
 }
 
 #' Panel widget
-#' @md
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' @description `r lifecycle::badge("experimental")`\cr
+#' Designed to be grouped using [`panel_group`] element. Used to handle `shiny` inputs in the encoding panel.
 #' @param title (`character`)\cr title of panel
 #' @param ... content of panel
 #' @param collapsed (`logical`, optional)\cr
@@ -48,6 +86,26 @@ panel_group <- function(..., id = NULL) {
 #'
 #' @return (`shiny.tag`)
 #'
+#' @examples
+#'
+#' library(shiny)
+#' panel_item(
+#'   title = "Display",
+#'   collapsed = FALSE,
+#'   checkboxGroupInput(
+#'     "check",
+#'     "Tables display",
+#'     choices = LETTERS[1:3],
+#'     selected = LETTERS[1]
+#'   ),
+#'   radioButtons(
+#'     "radio",
+#'     label = "Plot type",
+#'     choices = letters[1:2],
+#'     selected = letters[1]
+#'   )
+#' )
+#'
 #' @export
 panel_item <- function(title, ..., collapsed = TRUE, input_id = NULL) {
   stopifnot(checkmate::test_character(title, len = 1) || inherits(title, c("shiny.tag", "shiny.tag.list", "html")))

R/plot_with_settings.R

@@ -61,7 +61,7 @@ plot_with_settings_ui <- function(id) {
 #' Plot-with-settings module
 #'
 #' @rdname plot_with_settings
-#' @description `r lifecycle::badge("stable")`
+#' @description `r lifecycle::badge("stable")`\cr
 #' Universal module for plots with settings for height, width, and download.
 #'
 #' @export
@@ -596,15 +596,39 @@ type_download_srv <- function(id, plot_reactive, plot_type, plot_w, default_w, p
   )
 }
 
-#' Cleans and organizes output to account for NAs and remove empty rows.
+#' Clean brushed points
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description `r lifecycle::badge("stable")`\cr
+#' Cleans and organizes output to account for NAs and remove empty rows. Wrapper around `shiny::brushedPoints`.
 #' @param data (`data.frame`)\cr
-#'  A dataframe from which to select rows.
+#'  A data.frame from which to select rows.
 #' @param brush (`list`)\cr
-#'  The data from a brush e.g. input$plot_brush.
+#'  The data from a brush e.g. `input$plot_brush`.
+#'
+#' @return A `data.frame` of selected rows.
+#'
+#' @examples
+#'
+#' brush <- list(
+#'   mapping = list(
+#'     x = "AGE",
+#'     y = "BMRKR1"
+#'   ),
+#'   xmin = 30, xmax = 40,
+#'   ymin = 0.7, ymax = 10,
+#'   direction = "xy"
+#' )
+#'
+#' data <- data.frame(
+#'   STUDYID = letters[1:20],
+#'   USUBJID = LETTERS[1:20],
+#'   AGE = sample(25:40, size = 20, replace = TRUE),
+#'   BMRKR1 = runif(20, min = 0, max = 12)
+#' )
+#' nrow(clean_brushedPoints(data, brush))
+#' data$AGE[1:10] <- NA
+#' nrow(clean_brushedPoints(data, brush))
 #'
-#' @return A dataframe of selected rows.
 #' @export
 #'
 clean_brushedPoints <- function(data, brush) { # nolint object_name_linter.

R/standard_layout.R

@@ -1,8 +1,8 @@
-#' Create a standard UI layout with output on the right and an encoding panel on
-#' the left
+#' Standard UI layout
 #'
-#' @description `r lifecycle::badge("stable")`
-#' This is the layout used by the `teal` modules.
+#' @description `r lifecycle::badge("stable")`\cr
+#' Create a standard UI layout with output on the right and an encoding panel on
+#' the left. This is the layout used by the `teal` modules.
 #'
 #' @param output (`shiny.tag`)\cr
 #'   object with the output element (table, plot, listing) such as for example returned
@@ -19,6 +19,32 @@
 #'
 #' @return an object of class \code{shiny.tag} with the UI code.
 #'
+#' @examples
+#' library(shiny)
+#' standard_layout(
+#'   output = white_small_well(h3("Tests")),
+#'   encoding = div(
+#'     teal.reporter::simple_reporter_ui("simple_reporter"),
+#'     tags$label("Encodings", class = "text-primary"),
+#'     panel_item(
+#'       "Tests",
+#'       optionalSelectInput(
+#'         "tests",
+#'         "Tests:",
+#'         choices = c(
+#'           "Shapiro-Wilk",
+#'           "Kolmogorov-Smirnov (one-sample)"
+#'         ),
+#'         selected = "Shapiro-Wilk"
+#'       )
+#'     )
+#'   ),
+#'   forms = tagList(
+#'     verbatim_popup_ui("warning", "Show Warnings"),
+#'     verbatim_popup_ui("rcode", "Show R code")
+#'   )
+#' )
+#'
 #' @export
 standard_layout <- function(output,
                             encoding = NULL,

R/table_with_settings.R

@@ -1,8 +1,9 @@
 #' @name table_with_settings
 #'
-#' @title table_with_settings module
+#' @title `table_with_settings` module
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description `r lifecycle::badge("stable")`\cr
+#' Module designed to create a `shiny` table output based on `rtable` object (`ElementaryTable` or `TableTree`) input.
 #' @inheritParams shiny::moduleServer
 #' @param ... (`character`)\cr
 #'  Useful for providing additional HTML classes for the output tag.

R/white_small_well.R

@@ -1,6 +1,7 @@
-#' Adds Class Small Well and overflow-x property to HTML output element
+#' Small well class for HTML
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description `r lifecycle::badge("stable")`\cr
+#' Adds Small Well class and overflow-x property to HTML output element.
 #' @param ... other arguments to pass to tag object's div attributes.
 #'
 #' @details `white_small_well` is intended to be used with [shiny::uiOutput()].