minor changes.

R/all_choices.R

@@ -4,7 +4,7 @@
 #' `r lifecycle::badge("experimental")`
 #'
 #' An S3 structure representing the selection of all possible choices in a
-#' `filter_spec`, `select_spec` or `choices_selected` object
+#' `filter_spec`, `select_spec` or `choices_selected` object.
 #'
 #' @return `all_choices` object.
 #'

R/call_utils.R

@@ -1,6 +1,6 @@
 #' Checks `varname` argument and convert to call
 #'
-#' Checks `varname` type and parse if it's a `character`
+#' Checks `varname` type and parse if it's a `character`.
 #'
 #' @param varname (`name` or `call` or `character(1)`)
 #' name of the variable
@@ -35,22 +35,24 @@ call_check_parse_varname <- function(varname) {
 #'
 #' Compose choices condition call from inputs.
 #'
-#' @param varname (`name` or `call` or `character(1)`)
-#' name of the variable.
-#' @param choices (`vector`)
-#' `varname` values to match using the `==` (single value) or `%in%` (vector)
-#' condition.
+#' @details
 #' `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
+#' * `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`).
+#' 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 varname (`name` or `call` or `character(1)`)
+#' name of the variable.
+#' @param choices (`vector`)
+#' `varname` values to match using the `==` (single value) or `%in%` (vector)
+#' condition.
 #'
 #' @return `call`.
 #'

R/choices_labeled.R

@@ -120,10 +120,12 @@ choices_labeled <- function(choices, labels, subset = NULL, types = NULL) {
   )
 }
 
-#' Wrapper on [choices_labeled] to label variables basing on existing labels in data
+#' Variable label extraction and custom selection from data
 #'
+#' @description
 #' `r lifecycle::badge("stable")`
 #'
+#' Wrapper on [choices_labeled] to label variables basing on existing labels in data.
 #'
 #' @rdname variable_choices
 #'
@@ -240,10 +242,13 @@ variable_choices.data.frame <- function(data, subset = NULL, fill = TRUE, key =
   }
 }
 
-#' Wrapper on [choices_labeled] to label variable values basing on other variable values
+#' Value labeling and filtering based on variable relationship
 #'
+#' @description
 #' `r lifecycle::badge("stable")`
 #'
+#' Wrapper on [choices_labeled] to label variable values basing on other variable values.
+#'
 #' @rdname value_choices
 #'
 #' @param data (`data.frame`, `character`)
@@ -374,17 +379,11 @@ value_choices.data.frame <- function(data,
   res
 }
 
-#' Print choices_labeled object
-#'
-#' `r lifecycle::badge("stable")`
-#'
-#' @rdname choices_labeled
+#' @describeIn choices_labeled Print choices_labeled object
 #'
 #' @param x an object used to select a method.
 #' @param ... further arguments passed to or from other methods.
 #'
-#' @return `x`, invisibly.
-#'
 #' @export
 #'
 print.choices_labeled <- function(x, ...) {

R/choices_selected.R

@@ -9,7 +9,7 @@ no_select_keyword <- "-- no selection --"
 #' additional settings such as to order the choices with the selected elements appearing first
 #' or whether to block the user from making selections.
 #'
-#' Can be used in `ui` input elements such as [teal.widgets::optionalSelectInput()].
+#' Can be used in UI input elements such as [teal.widgets::optionalSelectInput()].
 #'
 #' @details
 #' Please note that the order of selected will always follow the order of choices. The `keep_order`
@@ -34,8 +34,8 @@ no_select_keyword <- "-- no selection --"
 #' be on top of the drop-down field.
 #' @param fixed (optional `logical`) Whether to block user to select choices.
 #'
-#' @return `choices_selected` returns object of class `choices_selected` and of
-#' type list which contains the specified `choices`, `selected`, `keep_order` and `fixed`.
+#' @return `choices_selected` returns list of `choices_selected`, encapsulating the specified
+#' `choices`, `selected`, `keep_order` and `fixed`.
 #'
 #' @examples
 #' library(shiny)
@@ -240,7 +240,10 @@ no_selected_as_NULL <- function(x) { # nolint: object_name_linter.
 }
 
 ## Non-exported utils functions ----
-## Modify vectors and keep attributes
+#' Modify vectors and keep attributes
+#' @keywords internal
+#' @noRd
+#'
 vector_reorder <- function(vec, idx) {
   checkmate::assert_atomic(vec)
   checkmate::assert_integer(idx, min.len = 1, lower = 1, any.missing = FALSE)

R/data.R

@@ -46,7 +46,7 @@
 #' @name rADSL
 "rADSL"
 
-#' Random Time to Event Analysis Dataset
+#' Random time to event analysis dataset
 #'
 #' @docType data
 #'

R/data_extract_datanames.R

@@ -8,7 +8,7 @@
 #'
 #' @param data_extracts (`list`) of data extracts for single variable.
 #'
-#' @return [shiny::helpText()] object.
+#' @return `shiny.tag` defining help-text element that can be added to a UI element.
 #'
 #' @export
 #'
@@ -26,7 +26,7 @@ datanames_input <- function(data_extracts) {
 #' `r lifecycle::badge("stable")`
 #'
 #' Fetches `dataname` slot per `data_extract_spec` from a list of
-#' `data_extract_spec` and returns the unique `dataname` set.
+#' `data_extract_spec`.
 #'
 #' @param data_extracts (`data_extract_spec(1)`) object or a list (of lists)
 #' of `data_extract_spec`.
@@ -64,9 +64,12 @@ get_extract_datanames <- function(data_extracts) {
   unique(unlist(datanames))
 }
 
-#' Checks if the input `data_extract_spec` objects all come from the same dataset
+#' Verify uniform dataset source across data extract specification
 #'
-#' `r lifecycle::badge("stable")`
+#' @description
+#'  `r lifecycle::badge("stable")`
+#'
+#' Checks if the input `data_extract_spec` objects all come from the same dataset.
 #'
 #' @param ... either `data_extract_spec` objects or lists of `data_extract_spec`
 #' objects that do not contain `NULL`

R/data_extract_module.R

@@ -590,7 +590,7 @@ data_extract_srv.list <- function(id,
 #'
 #' See example for details.
 #'
-#' @return reactive named list containing outputs from [data_extract_srv()].
+#' @return reactive named `list` containing outputs from [data_extract_srv()].
 #' Output list names are the same as `data_extract` input argument.
 #'
 #' @examples

R/data_extract_spec.R

@@ -1,13 +1,13 @@
-#' Data Extract input for `teal` modules
+#' Data extract input for `teal` modules
 #'
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' The Data Extract input can be used to filter and select columns from a data set.
+#' The Data extract input can be used to filter and select columns from a data set.
 #' This function enables such an input in `teal`.
 #' Please use the constructor function [data_extract_spec] to set it up.
 #'
-#' Note that no checks based on columns can be done because the data is only referred to by name.
+#' @note No checks based on columns can be done because the data is only referred to by name.
 #'
 #' @rdname data_extract_spec
 #'
@@ -22,7 +22,7 @@
 #' @param filter (`NULL` or `filter_spec` or its respective delayed version)
 #' Setup of the filtering of key columns inside the dataset.
 #' This setup can be created using the [filter_spec] function.
-#' Please note that if both select and filter are set to NULL, then the result
+#' Please note that if both select and filter are set to `NULL`, then the result
 #' will be a filter spec UI with all variables as possible choices and a select
 #' spec with multiple set to `TRUE`.
 #' @param reshape (`logical`)

R/filter_spec.R

@@ -3,7 +3,7 @@
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' It consists in choices and additionally the variable names for the choices
+#' It consists in choices and additionally the variable names for the choices.
 #'
 #' @details
 #' The `filter_spec` is used inside `teal` apps to allow filtering datasets

R/get_dplyr_call.R

@@ -1,7 +1,7 @@
 #' Aggregates data extract selectors
 #'
-#' Simplifies selector_list into aggregated list with one element per
-#' same selector - same dataset, same filter configuration and same reshape status
+#' Simplifies `selector_list` into aggregated list with one element per
+#' same selector - same dataset, same filter configuration and same reshape status.
 #'
 #' @inheritParams get_merge_call
 #'

R/get_merge_call.R

@@ -3,7 +3,7 @@
 #' @description
 #' `r lifecycle::badge("stable")`
 #'
-#' Returns list of calls depending on selector(s) and type of the merge.
+#' Creates list of calls depending on selector(s) and type of the merge.
 #' The merge order is the same as in selectors passed to the function.
 #'
 #' @inheritParams merge_datasets

R/include_css_js.R

@@ -2,8 +2,8 @@
 #'
 #' `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 a result, this method is individually redefined as required in each package.
+#' Therefore, this function is not exported.
 #'
 #' @param pattern (`character`) pattern of files to be included.
 #'

R/input_checks.R

@@ -29,7 +29,7 @@ list_extract_spec <- function(x, allow_null = FALSE) {
 #'
 #' `r lifecycle::badge("stable")`
 #'
-#' Stops if condition not met
+#' Stops if condition not met.
 #'
 #' @param extract_input (`list` or `NULL`) a list of `data_extract_spec`
 #'

R/merge_datasets.R

@@ -129,8 +129,6 @@ merge_datasets <- function(selector_list, datasets, join_keys, merge_function =
     SIMPLIFY = FALSE
   )
 
-  selector_datanames <- unique(vapply(merged_selector_list, `[[`, character(1), "dataname"))
-
   dplyr_calls <- lapply(seq_along(merged_selector_list), function(idx) {
     dplyr_call <- get_dplyr_call(
       selector_list = merged_selector_list,

R/merge_expression_module.R

@@ -1,8 +1,9 @@
 #' Merge expression module
 #'
+#' @description
 #' `r lifecycle::badge("experimental")`
 #'
-#' This function is a convenient wrapper to combine `data_extract_multiple_srv()` and
+#' Convenient wrapper to combine `data_extract_multiple_srv()` and
 #' `merge_expression_srv()` when no additional processing is required.
 #' Compare the example below with that found in [merge_expression_srv()].
 #'