Pre-release activities (#1021)

part of insightsengineering/nestdevs-tasks#48

- [x] Review and update:
      - README.md (check example code)
      - NEWS.md
- [x] Run urlchecker::url_check() to identify broken links and fix
- [x] Review functions:
       - @example tag, make sure it runs, fix if otherwise
- Make sure functions has @return tag to document the return value
       - no \dontrun tag, replace with if(interactive()) if needed
- [x] Sanity check of all vignettes, make sure there is no typo, no
wrong format, etc.
- [x] Run R CMD check --as-cran make sure everything pass
- [x] Package Title is not duplicated in Package Description in
DESCRIPTION file (e.g. this happens in teal.slice currently)
- [x] All package names in Title and Description fields of DESCRIPTION
file are quoted with '
- [x] You have checked the Package Release Template
https://github.com/insightsengineering/teal.reporter/pull/205/files
- [x] Make sure there are no ::: in examples
- [x] Make sure all teal.* mentions are lower-cased and quoted
- [x] Make Sure inst/WORDLIST is minimalized
- [x] Make sure non-exported functions do not have examples
- [x] Make sure each link to our documentation hosted with pkgdown on
github pages do not have /main/ in the address but it has /latest/
instead, so we always expose the documentation of the latest release and
not what's currently on main branch but not yet released
- [x] remove old rd syntax
- [x] switch from title case into sentence case for title and
descriotion of functions.

---------

Signed-off-by: kartikeya kirar <[email protected]>
Signed-off-by: Aleksander Chlebowski <[email protected]>
Signed-off-by: Vedha Viyash <[email protected]>
Signed-off-by: Marcin <[email protected]>
Signed-off-by: André Veríssimo <[email protected]>
Co-authored-by: Dawid Kałędkowski <[email protected]>
Co-authored-by: Aleksander Chlebowski <[email protected]>
Co-authored-by: go_gonzo <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Aleksander Chlebowski <[email protected]>
Co-authored-by: André Veríssimo <[email protected]>
Co-authored-by: Chendi Liao <[email protected]>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Dony Unardi <[email protected]>
Co-authored-by: vedhav <[email protected]>
Co-authored-by: Vedha Viyash <[email protected]>
Co-authored-by: Marcin <[email protected]>

.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
   )

DESCRIPTION

@@ -90,7 +90,6 @@ Collate:
     'module_tabs_with_filters.R'
     'module_teal.R'
     'module_teal_with_splash.R'
-    'modules_debugging.R'
     'reporter_previewer_module.R'
     'show_rcode_modal.R'
     'tdata.R'

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")`
-#' @inheritParams module
-#' @return A `teal` module which can be included in the `modules` argument to [teal::init()].
+#' `r lifecycle::badge("experimental")`
+#'
+#' @inheritParams teal_modules
+#' @return A `teal` module which can be included in the `modules` argument to [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

@@ -1,8 +1,8 @@
 #' Generates library calls from current session info
 #'
-#' Function to create multiple library calls out of current session info to make reproducible code works.
+#' Function to create multiple library calls out of current session info to ensure reproducible code works.
 #'
-#' @return Character object contain code
+#' @return Character vector of `library(<package>)` calls.
 #' @keywords internal
 get_rcode_libraries <- function() {
   vapply(
@@ -18,21 +18,20 @@ get_rcode_libraries <- function() {
     paste0(collapse = "")
 }
 
-
-
+#' @noRd
+#' @keywords internal
 get_rcode_str_install <- function() {
   code_string <- getOption("teal.load_nest_code")
-
-  if (!is.null(code_string) && is.character(code_string)) {
-    return(code_string)
+  if (is.character(code_string)) {
+    code_string
+  } else {
+    "# Add any code to install/load your NEST environment here\n"
   }
-
-  return("# Add any code to install/load your NEST environment here\n")
 }
 
 #' Get datasets code
 #'
-#' Get combined code from `FilteredData` and from `CodeClass` object.
+#' Retrieve complete code to create, verify, and filter a dataset.
 #'
 #' @param datanames (`character`) names of datasets to extract code from
 #' @param datasets (`FilteredData`) object

R/include_css_js.R

@@ -2,21 +2,20 @@
 #'
 #' `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
 #'
-#' @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", mustWork = TRUE),
     pattern = pattern, full.names = TRUE
   )
-  return(
-    shiny::singleton(
-      shiny::tags$head(lapply(css_files, shiny::includeCSS))
-    )
+
+  singleton(
+    tags$head(lapply(css_files, includeCSS))
   )
 }
 
@@ -29,14 +28,14 @@ include_css_files <- function(pattern = "*") {
 #' @param pattern (`character`) pattern of files to be included, passed to `system.file`
 #' @param except (`character`) vector of basename filenames to be excluded
 #'
-#' @return HTML code that includes `JS` files
+#' @return HTML code that includes `JS` files.
 #' @keywords internal
 include_js_files <- function(pattern = NULL, except = NULL) {
   checkmate::assert_character(except, min.len = 1, any.missing = FALSE, null.ok = TRUE)
   js_files <- list.files(system.file("js", package = "teal", mustWork = TRUE), pattern = pattern, full.names = TRUE)
   js_files <- js_files[!(basename(js_files) %in% except)] # no-op if except is NULL
 
-  return(singleton(lapply(js_files, includeScript)))
+  singleton(lapply(js_files, includeScript))
 }
 
 #' Run `JS` file from `/inst/js/` package directory
@@ -48,32 +47,38 @@ 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
+#' @param files (`character`) vector of filenames.
+#'
+#' @return returns `NULL`, invisibly.
 #' @keywords internal
 run_js_files <- function(files) {
   checkmate::assert_character(files, min.len = 1, any.missing = FALSE)
   lapply(files, function(file) {
     shinyjs::runjs(paste0(readLines(system.file("js", file, package = "teal", mustWork = TRUE)), collapse = "\n"))
   })
-  return(invisible(NULL))
+  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(