From 3210dd6bcd4113c8bb9b3d1979be09f06408f5b7 Mon Sep 17 00:00:00 2001
From: go_gonzo <dawid.kaledkowski@gmail.com>
Date: Fri, 6 Oct 2023 12:59:37 +0200
Subject: [PATCH] Fixing CRAN comments

---
 R/get_dt_rows.R                               | 32 +++++++++++-----
 R/optionalInput.R                             |  7 ++++
 R/plot_with_settings.R                        | 37 +++++++++++++------
 R/table_with_settings.R                       |  5 ++-
 man/get_dt_rows.Rd                            | 32 +++++++++++-----
 man/optionalSelectInput.Rd                    |  4 ++
 man/optionalSliderInput.Rd                    |  3 ++
 man/optionalSliderInputValMinMax.Rd           |  3 ++
 ..._settings_srv.Rd => plot_with_settings.Rd} | 33 +++++++++++++----
 man/plot_with_settings_ui.Rd                  | 14 -------
 man/table_with_settings.Rd                    |  5 ++-
 11 files changed, 119 insertions(+), 56 deletions(-)
 rename man/{plot_with_settings_srv.Rd => plot_with_settings.Rd} (94%)
 delete mode 100644 man/plot_with_settings_ui.Rd

diff --git a/R/get_dt_rows.R b/R/get_dt_rows.R
index 778575f6..c7c07b50 100644
--- a/R/get_dt_rows.R
+++ b/R/get_dt_rows.R
@@ -7,21 +7,33 @@
 #' @name get_dt_rows
 #'
 #' @examples
-#' \dontrun{
 #' library(shiny)
-#' # in Shiny UI function
-#' tagList(
-#'   get_dt_rows(ns("data_table"), ns("dt_rows")),
-#'   ...
-#' )
+#' ui <- function(id) {
+#'   ns <- NS(id)
+#'   tagList(
+#'     DT::DTOutput(ns("data_table")),
+#'     get_dt_rows(ns("data_table"), ns("dt_rows"))
+#'   )
+#' }
 #'
 #' # use the input$dt_rows in the Shiny Server function
-#' if (!is.null(input$dt_rows)) {
-#'   dt_args$options$pageLength <- input$dt_rows
-#' } # nolint
-#' do.call(DT::datatable, dt_args)
+#' server <- function(id) {
+#'   moduleServer(id, function(input, output, session) {
+#'     output$data_table <- DT::renderDataTable(
+#'       {
+#'         iris
+#'       },
+#'       options = list(pageLength = input$dt_rows)
+#'     )
+#'   })
 #' }
 #'
+#' if (interactive()) {
+#'   shinyApp(
+#'     ui = ui("my_table_module"),
+#'     server = function(input, output, session) server("my_table_module")
+#'   )
+#' }
 #' @export
 get_dt_rows <- function(dt_name, dt_rows) {
   tags$head(
diff --git a/R/optionalInput.R b/R/optionalInput.R
index 56a29098..e74a3719 100644
--- a/R/optionalInput.R
+++ b/R/optionalInput.R
@@ -26,6 +26,9 @@
 #' @param width (`character(1)`)\cr
 #'  The width of the input passed to `pickerInput`  e.g. `'auto'`, `'fit'`, `'100px'` or `'75%'`
 #'
+#' @return (`shiny.tag`) HTML tag with `pickerInput` widget and
+#'  non-interactive element listing selected values.
+#'
 #' @export
 #'
 #' @examples
@@ -471,6 +474,8 @@ extract_raw_choices <- function(choices, sep) {
 #'  an object of class `shiny.tag`. E.g. an object returned by [shiny::helpText()]
 #' @param ... optional arguments to `sliderInput`
 #'
+#' @return (`shiny.tag`) HTML tag with `sliderInput` widget.
+#'
 #' @export
 #'
 #' @examples
@@ -532,6 +537,8 @@ optionalSliderInput <- function(inputId, label, min, max, value, label_help = NU
 #'  Otherwise, if it is of length three the three elements will map to `value`, `min` and `max` of
 #'  the [optionalSliderInput()] function.
 #'
+#' @return (`shiny.tag`) HTML tag with range `sliderInput` widget.
+#'
 #' @export
 #'
 #' @examples
diff --git a/R/plot_with_settings.R b/R/plot_with_settings.R
index aa0fabc7..8a823f4c 100644
--- a/R/plot_with_settings.R
+++ b/R/plot_with_settings.R
@@ -1,9 +1,5 @@
-#' UI part of plot-with-settings module
-#'
-#' @description `r lifecycle::badge("stable")`
+#' @rdname plot_with_settings
 #' @export
-#'
-#' @param id (\code{character}) module ID
 plot_with_settings_ui <- function(id) {
   checkmate::assert_string(id)
 
@@ -62,12 +58,16 @@ plot_with_settings_ui <- function(id) {
   )
 }
 
-#' Server part of plot-with-settings module
+#' Plot-with-settings module
 #'
+#' @rdname plot_with_settings
 #' @description `r lifecycle::badge("stable")`
+#' Universal module for plots with settings for height, width, and download.
+#'
 #' @export
 #'
 #' @inheritParams shiny::moduleServer
+#'
 #' @param plot_r (`reactive` or `function`)\cr
 #'  `reactive` expression or a simple `function` to draw a plot.
 #'  A simple `function` is needed e.g. for base plots like `plot(1)` as the output can not be caught when downloading.
@@ -107,10 +107,9 @@ plot_with_settings_ui <- function(id) {
 #' If an invalid value is set then the default value is used and a warning is outputted to the console.
 #'
 #' @examples
-#' \dontrun{
 #' # Example using a reactive as input to plot_r
 #' library(shiny)
-#' shinyApp(
+#' app1 <- shinyApp(
 #'   ui = fluidPage(
 #'     plot_with_settings_ui(
 #'       id = "plot_with_settings"
@@ -130,8 +129,12 @@ plot_with_settings_ui <- function(id) {
 #'   }
 #' )
 #'
+#' if (interactive()) {
+#'   runApp(app1)
+#' }
+#'
 #' # Example using a function as input to plot_r
-#' shinyApp(
+#' app2 <- shinyApp(
 #'   ui = fluidPage(
 #'     radioButtons("download_option", "Select the Option", list("ggplot", "trellis", "grob", "base")),
 #'     plot_with_settings_ui(
@@ -167,8 +170,12 @@ plot_with_settings_ui <- function(id) {
 #'   }
 #' )
 #'
+#' if (interactive()) {
+#'   runApp(app2)
+#' }
+#'
 #' # Example with brushing/hovering/clicking/double-clicking
-#' shinyApp(
+#' app3 <- shinyApp(
 #'   ui = fluidPage(
 #'     plot_with_settings_ui(
 #'       id = "plot_with_settings"
@@ -202,10 +209,14 @@ plot_with_settings_ui <- function(id) {
 #'   }
 #' )
 #'
+#' if (interactive()) {
+#'   runApp(app3)
+#' }
+#'
 #' # Example which allows module to be hidden/shown
 #' library("shinyjs")
 #'
-#' shinyApp(
+#' app4 <- shinyApp(
 #'   ui = fluidPage(
 #'     useShinyjs(),
 #'     actionButton("button", "Show/Hide"),
@@ -229,7 +240,11 @@ plot_with_settings_ui <- function(id) {
 #'     )
 #'   }
 #' )
+#'
+#' if (interactive()) {
+#'   runApp(app4)
 #' }
+#'
 plot_with_settings_srv <- function(id,
                                    plot_r,
                                    height = c(600, 200, 2000),
diff --git a/R/table_with_settings.R b/R/table_with_settings.R
index adf29c13..1b7e0a2d 100644
--- a/R/table_with_settings.R
+++ b/R/table_with_settings.R
@@ -45,11 +45,10 @@ table_with_settings_ui <- function(id, ...) {
 #' @export
 #'
 #' @examples
-#' \dontrun{
 #' library(shiny)
 #' library(rtables)
 #' library(magrittr)
-#' shinyApp(
+#' app <- shinyApp(
 #'   ui = fluidPage(
 #'     table_with_settings_ui(
 #'       id = "table_with_settings"
@@ -69,6 +68,8 @@ table_with_settings_ui <- function(id, ...) {
 #'     table_with_settings_srv(id = "table_with_settings", table_r = table_r)
 #'   }
 #' )
+#' if (interactive()) {
+#'   runApp(app)
 #' }
 #'
 table_with_settings_srv <- function(id, table_r, show_hide_signal = reactive(TRUE)) {
diff --git a/man/get_dt_rows.Rd b/man/get_dt_rows.Rd
index 671be21d..1ada3f61 100644
--- a/man/get_dt_rows.Rd
+++ b/man/get_dt_rows.Rd
@@ -15,19 +15,31 @@ get_dt_rows(dt_name, dt_rows)
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 }
 \examples{
-\dontrun{
 library(shiny)
-# in Shiny UI function
-tagList(
-  get_dt_rows(ns("data_table"), ns("dt_rows")),
-  ...
-)
+ui <- function(id) {
+  ns <- NS(id)
+  tagList(
+    DT::DTOutput(ns("data_table")),
+    get_dt_rows(ns("data_table"), ns("dt_rows"))
+  )
+}
 
 # use the input$dt_rows in the Shiny Server function
-if (!is.null(input$dt_rows)) {
-  dt_args$options$pageLength <- input$dt_rows
-} # nolint
-do.call(DT::datatable, dt_args)
+server <- function(id) {
+  moduleServer(id, function(input, output, session) {
+    output$data_table <- DT::renderDataTable(
+      {
+        iris
+      },
+      options = list(pageLength = input$dt_rows)
+    )
+  })
 }
 
+if (interactive()) {
+  shinyApp(
+    ui = ui("my_table_module"),
+    server = function(input, output, session) server("my_table_module")
+  )
+}
 }
diff --git a/man/optionalSelectInput.Rd b/man/optionalSelectInput.Rd
index 6d333ff4..41e935d3 100644
--- a/man/optionalSelectInput.Rd
+++ b/man/optionalSelectInput.Rd
@@ -63,6 +63,10 @@ The width of the input passed to \code{pickerInput}  e.g. \code{'auto'}, \code{'
 
 \item{session}{(\code{shiny.session})\cr}
 }
+\value{
+(\code{shiny.tag}) HTML tag with \code{pickerInput} widget and
+non-interactive element listing selected values.
+}
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 Wrapper for \code{\link[shinyWidgets:pickerInput]{shinyWidgets::pickerInput()}} with additional features.
diff --git a/man/optionalSliderInput.Rd b/man/optionalSliderInput.Rd
index 851e6dff..cbdf2200 100644
--- a/man/optionalSliderInput.Rd
+++ b/man/optionalSliderInput.Rd
@@ -24,6 +24,9 @@ an object of class \code{shiny.tag}. E.g. an object returned by \code{\link[shin
 
 \item{...}{optional arguments to \code{sliderInput}}
 }
+\value{
+(\code{shiny.tag}) HTML tag with \code{sliderInput} widget.
+}
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 Hidden input widgets are useful to have the \code{input[[inputId]]} variable
diff --git a/man/optionalSliderInputValMinMax.Rd b/man/optionalSliderInputValMinMax.Rd
index 5f6aef52..4c89363b 100644
--- a/man/optionalSliderInputValMinMax.Rd
+++ b/man/optionalSliderInputValMinMax.Rd
@@ -28,6 +28,9 @@ an object of class \code{shiny.tag}. E.g. an object returned by \code{\link[shin
 
 \item{...}{optional arguments to \code{sliderInput}}
 }
+\value{
+(\code{shiny.tag}) HTML tag with range \code{sliderInput} widget.
+}
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 The \code{\link[=optionalSliderInput]{optionalSliderInput()}} function needs three arguments to determine
diff --git a/man/plot_with_settings_srv.Rd b/man/plot_with_settings.Rd
similarity index 94%
rename from man/plot_with_settings_srv.Rd
rename to man/plot_with_settings.Rd
index 29afcf8e..89ecff83 100644
--- a/man/plot_with_settings_srv.Rd
+++ b/man/plot_with_settings.Rd
@@ -1,9 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/plot_with_settings.R
-\name{plot_with_settings_srv}
+\name{plot_with_settings_ui}
+\alias{plot_with_settings_ui}
 \alias{plot_with_settings_srv}
-\title{Server part of plot-with-settings module}
+\title{Plot-with-settings module}
 \usage{
+plot_with_settings_ui(id)
+
 plot_with_settings_srv(
   id,
   plot_r,
@@ -65,6 +68,7 @@ the main page.}
 }
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
+Universal module for plots with settings for height, width, and download.
 }
 \details{
 By default the plot is rendered with \verb{72 dpi}. In order to change this, to for example 96 set
@@ -72,10 +76,9 @@ By default the plot is rendered with \verb{72 dpi}. In order to change this, to
 If an invalid value is set then the default value is used and a warning is outputted to the console.
 }
 \examples{
-\dontrun{
 # Example using a reactive as input to plot_r
 library(shiny)
-shinyApp(
+app1 <- shinyApp(
   ui = fluidPage(
     plot_with_settings_ui(
       id = "plot_with_settings"
@@ -95,8 +98,12 @@ shinyApp(
   }
 )
 
+if (interactive()) {
+  runApp(app1)
+}
+
 # Example using a function as input to plot_r
-shinyApp(
+app2 <- shinyApp(
   ui = fluidPage(
     radioButtons("download_option", "Select the Option", list("ggplot", "trellis", "grob", "base")),
     plot_with_settings_ui(
@@ -132,8 +139,12 @@ shinyApp(
   }
 )
 
+if (interactive()) {
+  runApp(app2)
+}
+
 # Example with brushing/hovering/clicking/double-clicking
-shinyApp(
+app3 <- shinyApp(
   ui = fluidPage(
     plot_with_settings_ui(
       id = "plot_with_settings"
@@ -167,10 +178,14 @@ shinyApp(
   }
 )
 
+if (interactive()) {
+  runApp(app3)
+}
+
 # Example which allows module to be hidden/shown
 library("shinyjs")
 
-shinyApp(
+app4 <- shinyApp(
   ui = fluidPage(
     useShinyjs(),
     actionButton("button", "Show/Hide"),
@@ -194,5 +209,9 @@ shinyApp(
     )
   }
 )
+
+if (interactive()) {
+  runApp(app4)
 }
+
 }
diff --git a/man/plot_with_settings_ui.Rd b/man/plot_with_settings_ui.Rd
deleted file mode 100644
index 2dd0fa07..00000000
--- a/man/plot_with_settings_ui.Rd
+++ /dev/null
@@ -1,14 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_with_settings.R
-\name{plot_with_settings_ui}
-\alias{plot_with_settings_ui}
-\title{UI part of plot-with-settings module}
-\usage{
-plot_with_settings_ui(id)
-}
-\arguments{
-\item{id}{(\code{character}) module ID}
-}
-\description{
-\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
-}
diff --git a/man/table_with_settings.Rd b/man/table_with_settings.Rd
index 0e689958..3a9c3534 100644
--- a/man/table_with_settings.Rd
+++ b/man/table_with_settings.Rd
@@ -27,11 +27,10 @@ a mechanism to allow modules which call this module to show/hide the table_with_
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}}
 }
 \examples{
-\dontrun{
 library(shiny)
 library(rtables)
 library(magrittr)
-shinyApp(
+app <- shinyApp(
   ui = fluidPage(
     table_with_settings_ui(
       id = "table_with_settings"
@@ -51,6 +50,8 @@ shinyApp(
     table_with_settings_srv(id = "table_with_settings", table_r = table_r)
   }
 )
+if (interactive()) {
+  runApp(app)
 }
 
 }