Pre-release activities

.lintr

@@ -1,6 +1,5 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
-  object_usage_linter = NULL,
-  indentation_linter = NULL
+  object_usage_linter = NULL
   )

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(c,teal_slices)
+S3method(format,teal_module)
+S3method(format,teal_modules)
 S3method(get_metadata,default)
 S3method(get_metadata,tdata)
 S3method(join_keys,tdata)
@@ -9,8 +11,6 @@ S3method(print,teal_modules)
 S3method(srv_nested_tabs,default)
 S3method(srv_nested_tabs,teal_module)
 S3method(srv_nested_tabs,teal_modules)
-S3method(toString,teal_module)
-S3method(toString,teal_modules)
 S3method(ui_nested_tabs,default)
 S3method(ui_nested_tabs,teal_module)
 S3method(ui_nested_tabs,teal_modules)

R/dummy_functions.R

@@ -1,81 +1,9 @@
-#' Get dummy `CDISC` data
-#'
-#' Get dummy `CDISC` data including `ADSL`, `ADAE` and `ADLB`.
-#' Some NAs are also introduced to stress test.
-#'
-#' @return `cdisc_data`
-#' @keywords internal
-example_cdisc_data <- function() { # nolint
-  ADSL <- data.frame( # nolint
-    STUDYID = "study",
-    USUBJID = 1:10,
-    SEX = sample(c("F", "M"), 10, replace = TRUE),
-    AGE = stats::rpois(10, 40)
-  )
-  ADTTE <- rbind(ADSL, ADSL, ADSL) # nolint
-  ADTTE$PARAMCD <- rep(c("OS", "EFS", "PFS"), each = 10) # nolint
-  ADTTE$AVAL <- c( # nolint
-    stats::rnorm(10, mean = 700, sd = 200), # dummy OS level
-    stats::rnorm(10, mean = 400, sd = 100), # dummy EFS level
-    stats::rnorm(10, mean = 450, sd = 200) # dummy PFS level
-  )
-
-  ADSL$logical_test <- sample(c(TRUE, FALSE, NA), size = nrow(ADSL), replace = TRUE) # nolint
-  ADSL$SEX[c(2, 5)] <- NA # nolint
-
-  res <- teal.data::cdisc_data(
-    ADSL = ADSL,
-    ADTTE = ADTTE,
-    code = '
-      ADSL <- data.frame(
-        STUDYID = "study",
-        USUBJID = 1:10,
-        SEX = sample(c("F", "M"), 10, replace = TRUE),
-        AGE = rpois(10, 40)
-      )
-      ADTTE <- rbind(ADSL, ADSL, ADSL)
-      ADTTE$PARAMCD <- rep(c("OS", "EFS", "PFS"), each = 10)
-      ADTTE$AVAL <- c(
-        rnorm(10, mean = 700, sd = 200),
-        rnorm(10, mean = 400, sd = 100),
-        rnorm(10, mean = 450, sd = 200)
-      )
-
-      ADSL$logical_test <- sample(c(TRUE, FALSE, NA), size = nrow(ADSL), replace = TRUE)
-      ADSL$SEX[c(2, 5)] <- NA
-    '
-  )
-  return(res)
-}
-
-#' Get datasets to go with example modules.
-#'
-#' Creates a nested list, the structure of which matches the module hierarchy created by `example_modules`.
-#' Each list leaf is the same `FilteredData` object.
-#'
-#' @return named list of `FilteredData` objects, each with `ADSL` set.
-#' @keywords internal
-example_datasets <- function() { # nolint
-  dummy_cdisc_data <- example_cdisc_data()
-  datasets <- teal_data_to_filtered_data(dummy_cdisc_data)
-  list(
-    "d2" = list(
-      "d3" = list(
-        "aaa1" = datasets,
-        "aaa2" = datasets,
-        "aaa3" = datasets
-      ),
-      "bbb" = datasets
-    ),
-    "ccc" = datasets
-  )
-}
-
 #' An example `teal` module
 #'
-#' @description `r lifecycle::badge("experimental")`
+#' `r lifecycle::badge("experimental")`
+#'
 #' @inheritParams module
-#' @return A `teal` module which can be included in the `modules` argument to [teal::init()].
+#' @return A `teal` module which can be included in the `modules` argument to [`teal::init()`].
 #' @examples
 #' app <- init(
 #'   data = teal_data(IRIS = iris, MTCARS = mtcars),
@@ -92,7 +20,6 @@ example_module <- function(label = "example teal module", datanames = "all") {
     server = function(id, data) {
       checkmate::assert_class(data(), "teal_data")
       moduleServer(id, function(input, output, session) {
-        ns <- session$ns
         updateSelectInput(session, "dataname", choices = isolate(teal.data::datanames(data())))
         output$text <- renderPrint({
           req(input$dataname)
@@ -101,7 +28,7 @@ example_module <- function(label = "example teal module", datanames = "all") {
         teal.widgets::verbatim_popup_srv(
           id = "rcode",
           verbatim_content = reactive(teal.code::get_code(data())),
-          title = "Association Plot"
+          title = "Example Code"
         )
       })
     },
@@ -118,30 +45,3 @@ example_module <- function(label = "example teal module", datanames = "all") {
     datanames = datanames
   )
 }
-
-
-#' Get example modules.
-#'
-#' Creates an example hierarchy of `teal_modules` from which a `teal` app can be created.
-#' @param datanames (`character`)\cr
-#'  names of the datasets to be used in the example modules. Possible choices are `ADSL`, `ADTTE`.
-#' @return `teal_modules`
-#' @keywords internal
-example_modules <- function(datanames = c("ADSL", "ADTTE")) {
-  checkmate::assert_subset(datanames, c("ADSL", "ADTTE"))
-  mods <- modules(
-    label = "d1",
-    modules(
-      label = "d2",
-      modules(
-        label = "d3",
-        example_module(label = "aaa1", datanames = datanames),
-        example_module(label = "aaa2", datanames = datanames),
-        example_module(label = "aaa3", datanames = datanames)
-      ),
-      example_module(label = "bbb", datanames = datanames)
-    ),
-    example_module(label = "ccc", datanames = datanames)
-  )
-  return(mods)
-}

R/get_rcode_utils.R

@@ -18,8 +18,8 @@ get_rcode_libraries <- function() {
     paste0(collapse = "")
 }
 
-
-
+#' @noRd
+#' @keywords internal
 get_rcode_str_install <- function() {
   code_string <- getOption("teal.load_nest_code")
 

R/include_css_js.R

@@ -2,7 +2,7 @@
 #'
 #' `system.file` should not be used to access files in other packages, it does
 #' not work with `devtools`. Therefore, we redefine this method in each package
-#' as needed. Thus, we do not export this method
+#' as needed. Thus, we do not export this method.
 #'
 #' @param pattern (`character`) pattern of files to be included
 #'
@@ -48,7 +48,7 @@ include_js_files <- function(pattern = NULL, except = NULL) {
 #'
 #' `system.file` should not be used to access files in other packages, it does
 #' not work with `devtools`. Therefore, we redefine this method in each package
-#' as needed. Thus, we do not export this method
+#' as needed. Thus, we do not export this method.
 #'
 #' @param files (`character`) vector of filenames
 #' @keywords internal
@@ -60,20 +60,24 @@ run_js_files <- function(files) {
   return(invisible(NULL))
 }
 
-#' Code to include teal `CSS` and `JavaScript` files
+#' Code to include `teal` `CSS` and `JavaScript` files
 #'
 #' This is useful when you want to use the same `JavaScript` and `CSS` files that are
-#' used with the teal application.
-#' This is also useful for running standalone modules in teal with the correct
+#' used with the `teal` application.
+#' This is also useful for running standalone modules in `teal` with the correct
 #' styles.
 #' Also initializes `shinyjs` so you can use it.
 #'
-#' @return HTML code to include
+#' Simply add `include_teal_css_js()` as one of the UI elements.
+#' @return A `shiny.tag.list`.
 #' @examples
+#' # use non-exported function from teal
+#' include_teal_css_js <- getFromNamespace("include_teal_css_js", "teal")
 #' shiny_ui <- tagList(
-#'   teal:::include_teal_css_js(),
+#'   include_teal_css_js(),
 #'   p("Hello")
 #' )
+#'
 #' @keywords internal
 include_teal_css_js <- function() {
   tagList(

R/init.R

@@ -4,44 +4,43 @@
 # error messages.
 
 
-#' Create the Server and UI Function For the Shiny App
+#' Create the server and UI function for the `shiny` app
 #'
 #' @description `r lifecycle::badge("stable")`
+#'
 #' End-users: This is the most important function for you to start a
-#' teal app that is composed out of teal modules.
+#' `teal` app that is composed out of `teal` modules.
 #'
 #' @details
 #' When initializing the `teal` app, if `datanames` are not set for the `teal_data` object,
 #' defaults from the `teal_data` environment will be used.
 #'
-#' @param data (`teal_data`, `teal_data_module`, `named list`)\cr
-#' `teal_data` object as returned by [teal.data::teal_data()] or
-#' `teal_data_module` or simply a list of a named list of objects
-#' (`data.frame` or `MultiAssayExperiment`).
-#' @param modules (`list`, `teal_modules` or `teal_module`)\cr
+#' @param data (`teal_data` or `teal_data_module`)
+#' `teal_data` object as returned by [`teal.data::teal_data()`] or `teal_data_module`.
+#' @param modules (`list` or `teal_modules` or `teal_module`)
 #'   nested list of `teal_modules` or `teal_module` objects or a single
 #'   `teal_modules` or `teal_module` object. These are the specific output modules which
-#'   will be displayed in the teal application. See [modules()] and [module()] for
+#'   will be displayed in the `teal` application. See [`modules()`] and [`module()`] for
 #'   more details.
-#' @param title (`shiny.tag` or `character(1)`)\cr
+#' @param title (`shiny.tag` or `character(1)`)
 #'   The browser window title. Defaults to a title "teal app" with the icon of NEST.
 #'   Can be created using the `build_app_title()` or
 #'   by passing a valid `shiny.tag` which is a head tag with title and link tag.
-#' @param filter (`teal_slices`)\cr
-#'   Specification of initial filter. Filters can be specified using [teal::teal_slices()].
+#' @param filter (`teal_slices`)
+#'   Specification of initial filter. Filters can be specified using [`teal::teal_slices()`].
 #'   Old way of specifying filters through a list is deprecated and will be removed in the
-#'   next release. Please fix your applications to use [teal::teal_slices()].
-#' @param header (`shiny.tag` or `character(1)`) \cr
+#'   next release. Please fix your applications to use [`teal::teal_slices()`].
+#' @param header (`shiny.tag` or `character(1)`)
 #'   The header of the app.
-#' @param footer (`shiny.tag` or `character(1)`)\cr
+#' @param footer (`shiny.tag` or `character(1)`)
 #'   The footer of the app.
-#' @param id (`character`)\cr
+#' @param id (`character`)
 #'   module id to embed it, if provided,
 #'   the server function must be called with [shiny::moduleServer()];
 #'   See the vignette for an example. However, [ui_teal_with_splash()]
 #'   is then preferred to this function.
 #'
-#' @return named list with `server` and `ui` function
+#' @return named list with server and UI function
 #'
 #' @export
 #'
@@ -119,14 +118,7 @@ init <- function(data,
       )
     )
   }
-  checkmate::assert(
-    .var.name = "data",
-    checkmate::check_multi_class(data, c("teal_data", "teal_data_module")),
-    checkmate::check_list(data, names = "named")
-  )
-  if (is.list(data) && !inherits(data, "teal_data_module")) {
-    data <- do.call(teal.data::teal_data, data)
-  }
+  checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
 
   ## `modules`
   checkmate::assert(
@@ -217,7 +209,7 @@ init <- function(data,
   ## `data` - `modules`
   if (inherits(data, "teal_data")) {
     if (length(teal_data_datanames(data)) == 0) {
-      stop("`data` object has no datanames and its environment is empty. Specify `datanames(data)` and try again.")
+      stop("The environment of `data` is empty.")
     }
     # in case of teal_data_module this check is postponed to the srv_teal_with_splash
     is_modules_ok <- check_modules_datanames(modules, teal_data_datanames(data))
@@ -236,7 +228,7 @@ init <- function(data,
 
   # Note regarding case `id = character(0)`:
   # rather than using `callModule` and creating a submodule of this module, we directly modify
-  # the `ui` and `server` with `id = character(0)` and calling the server function directly
+  # the UI and server with `id = character(0)` and calling the server function directly
   # rather than through `callModule`
   res <- list(
     ui = ui_teal_with_splash(id = id, data = data, title = title, header = header, footer = footer),

R/landing_popup_module.R

@@ -1,23 +1,24 @@
-#' Landing Popup Module
+#' Landing popup module
 #'
 #' @description Creates a landing welcome popup for `teal` applications.
 #'
 #' This module is used to display a popup dialog when the application starts.
 #' The dialog blocks the access to the application and must be closed with a button before the application is viewed.
 #'
-#' @param label `character(1)` the label of the module.
-#' @param title `character(1)` the text to be displayed as a title of the popup.
+#' @param label (`character(1)`) the label of the module.
+#' @param title (`character(1)`) the text to be displayed as a title of the popup.
 #' @param content The content of the popup. Passed to `...` of `shiny::modalDialog`. Can be a `character`
 #' or a list of `shiny.tag`s. See examples.
-#' @param buttons `shiny.tag` or a list of tags (`tagList`). Typically a `modalButton` or `actionButton`. See examples.
+#' @param buttons (`shiny.tag`) or a list of tags (`tagList`).
+#' Typically a `modalButton` or `actionButton`.See examples.
 #'
 #' @return A `teal_module` (extended with `teal_landing_module` class) to be used in `teal` applications.
 #'
 #' @examples
-#' app1 <- teal::init(
+#' app1 <- init(
 #'   data = teal_data(iris = iris),
-#'   modules = teal::modules(
-#'     teal::landing_popup_module(
+#'   modules = modules(
+#'     landing_popup_module(
 #'       content = "A place for the welcome message or a disclaimer statement.",
 #'       buttons = modalButton("Proceed")
 #'     ),
@@ -28,10 +29,10 @@
 #'   shinyApp(app1$ui, app1$server)
 #' }
 #'
-#' app2 <- teal::init(
+#' app2 <- init(
 #'   data = teal_data(iris = iris),
-#'   modules = teal::modules(
-#'     teal::landing_popup_module(
+#'   modules = modules(
+#'     landing_popup_module(
 #'       title = "Welcome",
 #'       content = tags$b(
 #'         "A place for the welcome message or a disclaimer statement.",