removing internal functions' examples (#198)

fixes: #181

Note: 

- `resolve` methods are exported but generic is internal so here example
of resolve is removed (resolve is used internally)
- Earlier this was done to pre-release which has been reverted

R/call_utils.R

@@ -56,16 +56,6 @@ call_check_parse_varname <- function(varname) {
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_condition_choice <- getFromNamespace("call_condition_choice", "teal.transform")
-#'
-#' call_condition_choice("SEX", choices = c(1, 2))
-#' call_condition_choice(as.name("SEX"), choices = "F")
-#' call_condition_choice("SEX", choices = c("F", "M"))
-#' call_condition_choice("SEX", choices = factor(c("F", "M")))
-#' call_condition_choice("x$SEX", choices = Sys.Date())
-#' call_condition_choice("trunc(x$SEX)", choices = Sys.time())
 #' @keywords internal
 #'
 call_condition_choice <- function(varname, choices) {
@@ -106,17 +96,6 @@ call_condition_choice <- function(varname, choices) {
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_condition_range <- getFromNamespace("call_condition_range", "teal.transform")
-#' call_extract_list <- getFromNamespace("call_extract_list", "teal.transform")
-#'
-#' call_condition_range("AGE", range = c(1, 2))
-#' call_condition_range(as.name("AGE"), range = c(-1.2, 2.1))
-#' call_condition_range(
-#'   call_extract_list("ADSL", "AGE"),
-#'   range = c(-1.2, 2.1)
-#' )
 #' @keywords internal
 #'
 call_condition_range <- function(varname, range) {
@@ -142,12 +121,6 @@ call_condition_range <- function(varname, range) {
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_condition_logical <- getFromNamespace("call_condition_logical", "teal.transform")
-#'
-#' call_condition_logical("event", choice = TRUE)
-#' call_condition_logical("event", choice = FALSE)
 #' @keywords internal
 #'
 call_condition_logical <- function(varname, choice) {
@@ -179,17 +152,6 @@ call_condition_logical <- function(varname, choice) {
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_condition_range_posixct <- getFromNamespace(
-#'   "call_condition_range_posixct", "teal.transform"
-#' )
-#'
-#' call_condition_range_posixct(
-#'   varname = as.name("datetime"),
-#'   range = c(Sys.time(), Sys.time() + 1),
-#'   timezone = "UTC"
-#' )
 #' @keywords internal
 #'
 call_condition_range_posixct <- function(varname, range, timezone = Sys.timezone()) {
@@ -222,14 +184,6 @@ call_condition_range_posixct <- function(varname, range, timezone = Sys.timezone
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_condition_range_date <- getFromNamespace("call_condition_range_date", "teal.transform")
-#'
-#' call_condition_range_date(
-#'   as.name("date"),
-#'   range = c(Sys.Date(), Sys.Date() + 1)
-#' )
 #' @keywords internal
 #'
 call_condition_range_date <- function(varname, range) {
@@ -256,21 +210,6 @@ call_condition_range_date <- function(varname, range) {
 #'
 #' @return [Extract()] `call` for 3-dimensional array in `x[i, j, k]` notation.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_extract_array <- getFromNamespace("call_extract_array", "teal.transform")
-#' call_condition_choice <- getFromNamespace("call_condition_choice", "teal.transform")
-#'
-#' call_extract_array(
-#'   dataname = "my_array",
-#'   row = call_condition_choice("my_array$SEX", "M"),
-#'   column = call("c", "SEX", "AGE"),
-#'   aisle = "RNAseq_rnaaccess"
-#' )
-#' call_extract_array(
-#'   "mae_object",
-#'   column = call_condition_choice("SEX", "M")
-#' )
 #' @keywords internal
 #'
 call_extract_array <- function(dataname = ".", row = NULL, column = NULL, aisle = NULL) {
@@ -319,20 +258,6 @@ call_extract_array <- function(dataname = ".", row = NULL, column = NULL, aisle
 #'
 #' @return [Extract()] `call` for matrix in `x[i, j]` notation.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_extract_matrix <- getFromNamespace("call_extract_matrix", "teal.transform")
-#' call_condition_choice <- getFromNamespace("call_condition_choice", "teal.transform")
-#'
-#' call_extract_matrix(
-#'   dataname = "my_array",
-#'   row = call_condition_choice("my_array$SEX", "M"),
-#'   column = call("c", "SEX", "AGE")
-#' )
-#' call_extract_matrix(
-#'   "mae_object",
-#'   column = call_condition_choice("SEX", "M")
-#' )
 #' @keywords internal
 #'
 call_extract_matrix <- function(dataname = ".", row = NULL, column = NULL) {
@@ -374,15 +299,6 @@ call_extract_matrix <- function(dataname = ".", row = NULL, column = NULL) {
 #'
 #' @return [Extract()] `call` in `$` or `[[` notation (depending on parameters).
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_extract_list <- getFromNamespace("call_extract_list", "teal.transform")
-#'
-#' call_extract_list("ADSL", "SEX")
-#' call_extract_list("ADSL", "named element")
-#' call_extract_list(as.name("ADSL"), as.name("AGE"))
-#' call_extract_list(as.name("weird name"), as.name("AGE"))
-#' call_extract_list(as.name("ADSL"), "AGE", dollar = FALSE)
 #' @keywords internal
 #'
 call_extract_list <- function(dataname, varname, dollar = TRUE) {
@@ -418,41 +334,6 @@ call_extract_list <- function(dataname, varname, dollar = TRUE) {
 #'
 #' @return `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' call_with_colon <- getFromNamespace("call_with_colon", "teal.transform")
-#'
-#' print_call_and_eval <- function(x) eval(print(x))
-#'
-#' print_call_and_eval(
-#'   call_with_colon("glue::glue", "x = {x}", x = 10)
-#' )
-#'
-#' # mtcars$cyl evaluated
-#' print_call_and_eval(
-#'   call_with_colon("dplyr::filter", as.name("mtcars"), mtcars$cyl == 6)
-#' )
-#'
-#' # mtcars$cyl argument not evaluated immediately (in call expression)
-#' print_call_and_eval(
-#'   call_with_colon("dplyr::filter", as.name("mtcars"), quote(cyl == 6))
-#' )
-#'
-#' # does not work because argument is evaluated and the
-#' # non-dplyr filter does not look inside mtcars
-#' # cannot eval because it does not pass checks because of non-standard evaluation
-#' call("filter", as.name("mtcars"), quote(cyl == 6))
-#' # works, but non-dplyr filter is taken
-#' call("filter", as.name("mtcars"), mtcars$cyl == 6)
-#'
-#' nb_args <- function(...) nargs()
-#' print_call_and_eval(
-#'   call_with_colon("nb_args", arg1 = 1, unlist_args = list(arg2 = 2, args3 = 3))
-#' )
-#' # duplicate arguments
-#' print_call_and_eval(
-#'   call_with_colon("nb_args", arg1 = 1, unlist_args = list(arg2 = 2, args2 = 2))
-#' )
 #' @keywords internal
 #'
 call_with_colon <- function(name, ..., unlist_args = list()) {
@@ -474,21 +355,6 @@ call_with_colon <- function(name, ..., unlist_args = list()) {
 #'
 #' @return A combined `call`.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' calls_combine_by <- getFromNamespace("calls_combine_by", "teal.transform")
-#' call_condition_choice <- getFromNamespace("call_condition_choice", "teal.transform")
-#' call_condition_range <- getFromNamespace("call_condition_range", "teal.transform")
-#'
-#' calls_combine_by(
-#'   "&",
-#'   calls = list(
-#'     call_condition_choice("SEX", "F"),
-#'     call_condition_range("AGE", c(20, 50)),
-#'     call_condition_choice("ARM", "ARM: A"),
-#'     TRUE
-#'   )
-#' )
 #' @keywords internal
 #'
 calls_combine_by <- function(operator, calls) {

R/data_extract_filter_module.R

@@ -8,11 +8,6 @@
 #'
 #' @return `shiny.tag` defining the `filter_spec`'s UI element.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' data_extract_filter_ui <- getFromNamespace("data_extract_filter_ui", "teal.transform")
-#'
-#' data_extract_filter_ui(filter = filter_spec(vars = "test_var"), id = "test_id")
 #' @keywords internal
 #'
 data_extract_filter_ui <- function(filter, id = "filter") {
@@ -141,18 +136,6 @@ data_extract_filter_srv <- function(id, datasets, filter) {
 #'
 #' @return named `list` with two slots `choices` and `selected`.
 #'
-#' @examples
-#' library(shiny)
-#' # use non-exported function from teal.transform
-#' get_initial_filter_values <- getFromNamespace("get_initial_filter_values", "teal.transform")
-#'
-#' filtered_data_list <- list(iris = reactive(head(iris)))
-#' filter <- filter_spec(vars = colnames(iris)[1])
-#' filter$dataname <- "iris"
-#' isolate(
-#'   get_initial_filter_values(filter = filter, datasets = filtered_data_list)
-#' )
-#'
 #' @keywords internal
 #'
 get_initial_filter_values <- function(filter, datasets) {

R/data_extract_module.R

@@ -34,15 +34,6 @@ id_for_dataset <- function(dataname) {
 #'
 #' @return `shiny.tag` with the HTML code for the panel.
 #'
-#' @examples
-#' library(shiny)
-#' # use non-exported function from teal.transform
-#' cond_data_extract_single_ui <- getFromNamespace("cond_data_extract_single_ui", "teal.transform")
-#'
-#' cond_data_extract_single_ui(
-#'   NS("TEST"),
-#'   data_extract_spec(dataname = "test")
-#' )
 #' @keywords internal
 #'
 cond_data_extract_single_ui <- function(ns, single_data_extract_spec) {

R/data_extract_select_module.R

@@ -7,14 +7,6 @@
 #'
 #' @return `shiny.tag.list` with the UI.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' data_extract_select_ui <- getFromNamespace("data_extract_select_ui", "teal.transform")
-#'
-#' data_extract_select_ui(
-#'   select = select_spec(choices = "test_choice"),
-#'   id = "test_id"
-#' )
 #' @keywords internal
 #'
 data_extract_select_ui <- function(select, id = "select") {

R/data_extract_single_module.R

@@ -10,11 +10,6 @@
 #'
 #' @return `shiny.tag` the HTML element defining the UI.
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' data_extract_single_ui <- getFromNamespace("data_extract_single_ui", "teal.transform")
-#'
-#' data_extract_single_ui(id = "test", data_extract_spec("extract"))
 #' @keywords internal
 #'
 data_extract_single_ui <- function(id = NULL, single_data_extract_spec) {

R/filter_spec.R

@@ -208,28 +208,6 @@ filter_spec <- function(vars,
 #'
 #' @seealso filter_spec
 #'
-#' @examples
-#' # use non-exported function from teal.transform
-#' filter_spec_internal <- getFromNamespace("filter_spec_internal", "teal.transform")
-#'
-#' filter_spec_internal(
-#'   vars_choices = c("PARAMCD", "AVISIT"),
-#'   vars_selected = "PARAMCD",
-#'   vars_multiple = TRUE
-#' )
-#'
-#' ADRS <- teal.transform::rADRS
-#' filter_spec_internal(
-#'   vars_choices = variable_choices(ADRS),
-#'   vars_selected = "PARAMCD",
-#'   vars_multiple = TRUE
-#' )
-#'
-#' filter_spec_internal(
-#'   vars_choices = variable_choices("ADRS"),
-#'   vars_selected = "PARAMCD",
-#'   vars_multiple = TRUE
-#' )
 #' @keywords internal
 #'
 filter_spec_internal <- function(vars_choices,