no old Rd tags - partial

R/call_utils.R

@@ -31,23 +31,24 @@ call_check_parse_varname <- function(varname) {
 #'
 #' Compose choices condition call from inputs.
 #'
-#' @param varname (`name`, `call` or `character(1)`)\cr
-#'   name of the variable
+#' @param varname (`name`, `call` or `character(1)`)
+#' name of the variable
+#' @param choices (`vector`)
+#' `varname` values to match using the `==` (single value) or `%in%` (vector)
+#' condition.
+#' `choices` can be vector of any type but for some output might be converted:
+#' * `factor` call is composed on choices converted to `character`
+#' * `Date` call is composed on choices converted to `character` using
+#' `format(choices)`
+#' * `POSIXct`, `POSIXlt` Call is composed on choices converted to `character` using
+#' `format(choices)`.
+#'
+#'     One has to be careful here as formatted date-time variable might loose
+#'     some precision (see `format` argument in [format.POSIXlt()] and output call
+#'     could be insufficient for exact comparison. In this case one should specify
+#'     `varname = trunc(<varname>)` and possibly convert `choices` to `character`)
 #'
-#' @param choices (`vector`)\cr
-#'   `varname` values to match using the `==` (single value) or
-#'   `%in%` (vector) condition. `choices` can be vector of any type
-#'   but for some output might be converted:
-#'   \itemize{
-#'     \item{`factor`}{ call is composed on choices converted to `character`}
-#'     \item{`Date`}{ call is composed on choices converted to `character` using `format(choices)`}
-#'     \item{`POSIXct`, `POSIXlt`}{ Call is composed on choices converted to `character` using
-#'       `format(choices)`. One has to be careful here as formatted date-time variable might loose
-#'       some precision (see `format` argument in \code{\link{format.POSIXlt}}) and output call
-#'       could be insufficient for exact comparison. In this case one should specify
-#'       `varname = trunc(<varname>)` and possibly convert `choices` to `character`)
-#'     }
-#'   }
+#' @return a `call`
 #'
 #' @examples
 #' # use non-exported function from teal.transform
@@ -59,7 +60,6 @@ call_check_parse_varname <- function(varname) {
 #' 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())
-#' @return a `call`
 #' @keywords internal
 #'
 call_condition_choice <- function(varname, choices) {
@@ -92,13 +92,16 @@ call_condition_choice <- function(varname, choices) {
 #'
 #' Compose `numeric` range condition call from inputs
 #'
-#' @param varname (`name` or `character(1)`)\cr
-#'   name of the variable
+#' @param varname (`name` or `character(1)`)
 #'
-#' @param range (`numeric(2)`)\cr
-#'   range of the variable
+#' name of the variable
+#'
+#' @param range (`numeric(2)`)
+#'
+#' range of the variable
+#'
+#' @return a `call`
 #'
-#' @return call
 #' @examples
 #' # use non-exported function from teal.transform
 #' call_condition_range <- getFromNamespace("call_condition_range", "teal.transform")
@@ -110,7 +113,6 @@ call_condition_choice <- function(varname, choices) {
 #'   call_extract_list("ADSL", "AGE"),
 #'   range = c(-1.2, 2.1)
 #' )
-#' @return a `call`
 #' @keywords internal
 #'
 call_condition_range <- function(varname, range) {
@@ -128,20 +130,22 @@ call_condition_range <- function(varname, range) {
 #'
 #' Compose `logical` variable condition call from inputs
 #'
-#' @param varname (`name` or `character(1)`)\cr
-#'   name of the variable
+#' @param varname (`name` or `character(1)`)
+#'
+#' name of the variable
 #'
-#' @param choice (`logical(1)`)\cr
-#'   chosen value
+#' @param choice (`logical(1)`)
+#'
+#' chosen value
+#'
+#' @return a `call`
 #'
-#' @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)
-#' @return a `call`
 #' @keywords internal
 #'
 call_condition_logical <- function(varname, choice) {
@@ -165,17 +169,16 @@ call_condition_logical <- function(varname, choice) {
 #'
 #' Compose `POSIXct` range condition call from inputs.
 #'
-#' @param varname (`name` or `character(1)`)\cr
-#'   name of the variable
+#' @param varname (`name` or `character(1)`)
+#' name of the variable
 #'
-#' @param range (`POSIXct`)\cr
-#'   range of the variable. Be aware that output
-#'   uses truncated range format `"%Y-%m-%d %H:%M:%S"`, which means that
-#'   some precision might be lost.
+#' @param range (`POSIXct`)
+#' range of the variable. Be aware that output uses truncated range format
+#' `"%Y-%m-%d %H:%M:%S"`, which means that some precision might be lost.
 #'
-#' @param timezone (`character(1)`)\cr
-#'   specifies the time zone to be used for the conversion.
-#'   By default `Sys.timezone()` is used.
+#' @param timezone (`character(1)`)
+#' specifies the time zone to be used for the conversion.
+#' By default `Sys.timezone()` is used.
 #'
 #' @examples
 #' # use non-exported function from teal.transform
@@ -216,11 +219,13 @@ call_condition_range_posixct <- function(varname, range, timezone = Sys.timezone
 #'
 #' Compose `Date` range condition call from inputs
 #'
-#' @param varname (`name` or `character(1)`)\cr
-#'   name of the variable
+#' @param varname (`name` or `character(1)`)
+#' name of the variable
 #'
-#' @param range (`Date`)\cr
-#'   range of the variable
+#' @param range (`Date`)
+#' range of the variable
+#'
+#' @return a `call`
 #'
 #' @examples
 #' # use non-exported function from teal.transform
@@ -230,7 +235,6 @@ call_condition_range_posixct <- function(varname, range, timezone = Sys.timezone
 #'   as.name("date"),
 #'   range = c(Sys.Date(), Sys.Date() + 1)
 #' )
-#' @return a `call`
 #' @keywords internal
 #'
 call_condition_range_date <- function(varname, range) {
@@ -247,15 +251,16 @@ call_condition_range_date <- function(varname, range) {
 
 #' Get call to subset and select array
 #'
-#' Get call to subset and select array
-#' @param dataname (`character(1)` or `name`)\cr
-#' @param row (`name`, `call`, `logical`, `integer`, `character`)\cr
-#'   optional, name of the `row` or condition
-#' @param column (`name`, `call`, `logical`, `integer`, `character`)\cr
-#'   optional, name of the `column` or condition
-#' @param aisle (`name`, `call`, `logical`, `integer`, `character`)\cr
-#'   optional, name of the `row` or condition
-#' @return `[` call with all conditions included
+#' @param dataname (`character(1)` or `name`)
+#' @param row (`name`, `call`, `logical`, `integer`, `character`)
+#' optional, name of the `row` or condition
+#' @param column (`name`, `call`, `logical`, `integer`, `character`)
+#' optional, name of the `column` or condition
+#' @param aisle (`name`, `call`, `logical`, `integer`, `character`)
+#' optional, name of the `row` or condition
+#'
+#' @return specific [Extract()] `call` for 3-dimensional array
+#'
 #' @examples
 #' # use non-exported function from teal.transform
 #' call_extract_array <- getFromNamespace("call_extract_array", "teal.transform")
@@ -271,7 +276,6 @@ call_condition_range_date <- function(varname, range) {
 #'   "mae_object",
 #'   column = call_condition_choice("SEX", "M")
 #' )
-#' @return specific \code{\link[base]{Extract}} `call` for 3-dimensional array
 #' @keywords internal
 #'
 call_extract_array <- function(dataname = ".", row = NULL, column = NULL, aisle = NULL) {
@@ -312,13 +316,14 @@ call_extract_array <- function(dataname = ".", row = NULL, column = NULL, aisle
 
 #' Get call to subset and select matrix
 #'
-#' Get call to subset and select matrix
-#' @param dataname (`character(1)` or `name`)\cr
-#' @param row (`name`, `call`, `logical`, `integer`, `character`)\cr
-#'   optional, name of the `row` or condition
-#' @param column (`name`, `call`, `logical`, `integer`, `character`)\cr
-#'   optional, name of the `column` or condition
-#' @return `[` call with all conditions included
+#' @param dataname (`character(1)` or `name`)
+#' @param row (`name`, `call`, `logical`, `integer`, `character`)
+#' optional, name of the `row` or condition
+#' @param column (`name`, `call`, `logical`, `integer`, `character`)
+#' optional, name of the `column` or condition
+#'
+#' @return specific [Extract()] `call` for matrix
+#'
 #' @examples
 #' # use non-exported function from teal.transform
 #' call_extract_matrix <- getFromNamespace("call_extract_matrix", "teal.transform")
@@ -333,7 +338,6 @@ call_extract_array <- function(dataname = ".", row = NULL, column = NULL, aisle
 #'   "mae_object",
 #'   column = call_condition_choice("SEX", "M")
 #' )
-#' @return specific \code{\link[base]{Extract}} `call` for matrix
 #' @keywords internal
 #'
 call_extract_matrix <- function(dataname = ".", row = NULL, column = NULL) {
@@ -369,18 +373,15 @@ call_extract_matrix <- function(dataname = ".", row = NULL, column = NULL) {
 
 #' Compose extract call with `$` operator
 #'
-#' Compose extract call with `$` operator
-#'
-#' @param dataname (`character(1)` or `name`)\cr
-#'   name of the object
-#'
-#' @param varname (`character(1)` or `name`)\cr
-#'   name of the slot in data
-#'
+#' @param dataname (`character(1)` or `name`)
+#' name of the object
+#' @param varname (`character(1)` or `name`)
+#' name of the slot in data
 #' @param dollar (`logical(1)`)\cr
-#'   whether returned call should use `$` or `[[` operator
+#' whether returned call should use `$` or `[[` operator
 #'
 #' @return `$` or `[[` call
+#'
 #' @examples
 #' # use non-exported function from teal.transform
 #' call_extract_list <- getFromNamespace("call_extract_list", "teal.transform")
@@ -474,13 +475,14 @@ call_with_colon <- function(name, ..., unlist_args = list()) {
 #'
 #' Combine list of calls by specific operator
 #'
-#' @param operator (`character(1)` or `name`)\cr
-#'   name/symbol of the operator.
+#' @param operator (`character(1)` or `name`)
+#' name / symbol of the operator.
+#'
+#' @param calls (`list` of calls)
+#' list containing calls to be combined by `operator`
 #'
-#' @param calls (`list` of calls)\cr
-#'   list containing calls to be combined by `operator`
+#' @return a combined `call`
 #'
-#' @return call
 #' @examples
 #' # use non-exported function from teal.transform
 #' calls_combine_by <- getFromNamespace("calls_combine_by", "teal.transform")
@@ -496,7 +498,6 @@ call_with_colon <- function(name, ..., unlist_args = list()) {
 #'     TRUE
 #'   )
 #' )
-#' @return a combined `call`
 #' @keywords internal
 #'
 calls_combine_by <- function(operator, calls) {

R/choices_selected.R

@@ -8,16 +8,19 @@ no_select_keyword <- "-- no selection --"
 #'   or whether to block the user from making selections. Can be used in `ui` input elements
 #'   such as [teal.widgets::optionalSelectInput()]
 #'
-#' @param choices (`character`) vector of possible choices or `delayed_data` object\cr
-#'   See [variable_choices()] and [value_choices()].
+#' @param choices (`character`) vector of possible choices or `delayed_data` object
+#'
+#' See [variable_choices()] and [value_choices()].
 #' @param selected (`character`) vector of preselected options, (`all_choices`) object
-#'  or (`delayed_data`) object. If `delayed_data` object then `choices` must also be
-#'  a `delayed_data` object. If not supplied it will default to the first element of
-#'  `choices` if `choices` is a vector, or `NULL` if `choices` is a `delayed_data` object.
-#' @param keep_order (`logical`)\cr
-#'  In case of `FALSE` the selected variables will be on top of the drop-down field.
-#' @param fixed optional, (`logical`)\cr
-#'  Whether to block user to select choices
+#' or (`delayed_data`) object.
+#'
+#' If `delayed_data` object then `choices` must also be `delayed_data` object.
+#' If not supplied it will default to the first element of `choices` if
+#' `choices` is a vector, or `NULL` if `choices` is a `delayed_data` object.
+#' @param keep_order (`logical`)
+#' In case of `FALSE` the selected variables will be on top of the drop-down field.
+#' @param fixed optional, (`logical`)
+#' Whether to block user to select choices
 #'
 #' @details
 #'
@@ -183,8 +186,8 @@ is.choices_selected <- function(x) { # nolint
 #'
 #' @description `r lifecycle::badge("stable")`
 #'
-#' @param x (\code{choices_selected}) output
-#' @param multiple (\code{logical}) whether multiple selections are allowed or not
+#' @param x (`choices_selected`) output
+#' @param multiple (`logical`) whether multiple selections are allowed or not
 #'
 #' @export
 add_no_selected_choices <- function(x, multiple = FALSE) {
@@ -206,10 +209,9 @@ add_no_selected_choices <- function(x, multiple = FALSE) {
 #'
 #' @description `r lifecycle::badge("stable")`
 #'
-#' @param x (\code{character}) Word that shall be checked for
-#'   NULL, empty, "--no-selection"
+#' @param x (`character`) Word that shall be checked for `NULL`, empty, "--no-selection"
 #'
-#' @return the word or NULL
+#' @return the word or `NULL`
 #'
 #' @export
 no_selected_as_NULL <- function(x) { # nolint

R/column_functions.R

@@ -3,12 +3,12 @@
 #' @description `r lifecycle::badge("stable")`
 #' @export
 #'
-#' @param data (\code{data.frame}) Data with attribute \code{filter_and_columns}. This can only be
-#'  created by \code{\link{data_extract_srv}}. which returns a shiny \code{\link[shiny]{reactive}}.
+#' @param data (`data.frame`) Data with attribute `filter_and_columns`. This can only be
+#' created by [data_extract_srv()]. which returns a shiny [shiny::reactive()].
 #'
-#' @return A named character vector with the non-key columns of the \code{data}..
+#' @return A named character vector with the non-key columns of the `data`.
 #'
-#' @references \link{data_extract_srv}
+#' @references [data_extract_srv]
 get_dataset_prefixed_col_names <- function(data) {
   if (!is.null(attr(data, "filter_and_columns")$columns) && attr(data, "filter_and_columns")$columns != "") {
     paste(attr(data, "dataname"), attr(data, "filter_and_columns")$columns, sep = ".")

R/data_extract_datanames.R

@@ -1,9 +1,13 @@
 #' Available datasets input
 #'
-#' @description `r lifecycle::badge("stable")`
+#' @description
+#' `r lifecycle::badge("stable")`
+#'
 #' Creates \link[shiny]{helpText} with the names of datasets
 #' available for current module.
+#'
 #' @param data_extracts list of data extracts for single variable
+#'
 #' @export
 datanames_input <- function(data_extracts) {
   datanames <- get_extract_datanames(data_extracts)
@@ -15,11 +19,14 @@ datanames_input <- function(data_extracts) {
 
 #' Gets names of the datasets from a list of `data_extract_spec` objects
 #'
-#' @description `r lifecycle::badge("stable")`
-#' Fetches `dataname` slot per \code{data_extract_spec} from a list of \code{data_extract_spec}
-#' and returns the unique `dataname` set.
+#' @description
+#' `r lifecycle::badge("stable")`
+#'
+#' Fetches `dataname` slot per `data_extract_spec` from a list of
+#' `data_extract_spec` and returns the unique `dataname` set.
 #'
-#' @param data_extracts A single \code{data_extract_spec} object or a list (of lists) of \code{data_extract_spec}
+#' @param data_extracts A single `data_extract_spec` object or a list (of lists)
+#' of `data_extract_spec`
 #'
 #' @export
 get_extract_datanames <- function(data_extracts) {
@@ -53,10 +60,13 @@ get_extract_datanames <- function(data_extracts) {
 
 #' Checks if the input `data_extract_spec` objects all come from the same dataset
 #'
-#' @description `r lifecycle::badge("stable")`
-#' @param ... either \code{data_extract_spec} objects or lists of \code{data_extract_spec} objects that do not contain
+#' `r lifecycle::badge("stable")`
+#'
+#' @param ... either `data_extract_spec` objects or lists of `data_extract_spec` objects that do not contain
 #'   NULL
+#'
 #' @return logical
+#'
 #' @export
 is_single_dataset <- function(...) {
   data_extract_spec <- list(...)