mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-23 05:50:21 +01:00
complete copy/paste from forcats and haven
This commit is contained in:
parent
8aa1ec41dc
commit
18544ddcfe
@ -61,7 +61,7 @@ Imports:
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openxlsx2,
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readODS,
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forcats,
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rlang
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vctrs
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Collate:
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'REDCapCAST-package.R'
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'utils.r'
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@ -1,6 +1,7 @@
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# Generated by roxygen2: do not edit by hand
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S3method(as_factor,character)
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S3method(as_factor,factor)
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S3method(as_factor,haven_labelled)
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S3method(as_factor,labelled)
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S3method(as_factor,logical)
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@ -59,6 +60,5 @@ importFrom(keyring,key_set)
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importFrom(openxlsx2,read_xlsx)
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importFrom(purrr,reduce)
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importFrom(readr,parse_time)
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importFrom(rlang,check_dots_used)
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importFrom(tidyr,pivot_wider)
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importFrom(tidyselect,all_of)
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204
R/as_factor.R
204
R/as_factor.R
@ -5,70 +5,145 @@
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#' ta loss in case of rich formatted and labelled data.
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#'
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#' Please refer to parent functions for extended documentation.
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#' To avoid redundancy calls and errors, functions are copy-pasted here
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#'
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#' @param x Object to coerce to a factor.
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#' @param ... Other arguments passed down to method.
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#' @export
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#' @examples
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#' # will preserve all attributes but class
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#' \dontrun{
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#' # will preserve all attributes
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#' c(1, 4, 3, "A", 7, 8, 1) |> as_factor()
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#' structure(c(1, 2, 3, 2, 10, 9),
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#' labels = c(Unknown = 9, Refused = 10)
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#' ) |>
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#' as_factor()
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#' as_factor() |> dput()
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#'
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#' structure(c(1, 2, 3, 2, 10, 9),
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#' labels = c(Unknown = 9, Refused = 10),
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#' class = "haven_labelled"
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#' ) |>
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#' as_factor()
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#' }
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#' @importFrom forcats as_factor
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#' @importFrom rlang check_dots_used
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#' @export
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#' @name as_factor
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as_factor <- function(x, ...) {
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rlang::check_dots_used()
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UseMethod("as_factor")
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}
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#' @rdname as_factor
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#' @export
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as_factor.factor <- function(x, ...) {
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x
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}
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#' @rdname as_factor
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#' @export
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as_factor.logical <- function(x, ...) {
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labels <- get_attr(x)
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x <- forcats::as_factor(x, ...)
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set_attr(x, labels[-match("class", names(labels))])
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x <- factor(x, levels = c("FALSE", "TRUE"))
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set_attr(x, labels, overwrite = FALSE)
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}
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#' @rdname as_factor
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#' @export
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as_factor.numeric <- function(x, ...) {
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labels <- get_attr(x)
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x <- forcats::as_factor(x, ...)
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set_attr(x, labels[-match("class", names(labels))])
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x <- factor(x)
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set_attr(x, labels, overwrite = FALSE)
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}
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#' @rdname as_factor
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#' @export
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as_factor.character <- function(x, ...) {
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labels <- get_attr(x)
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x <- forcats::as_factor(x, ...)
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set_attr(x, labels[-match("class", names(labels))])
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x <- structure(
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forcats::fct_inorder(x),
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label = attr(x, "label", exact = TRUE)
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)
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set_attr(x, labels, overwrite = FALSE)
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}
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#' @param ordered If `TRUE` create an ordered (ordinal) factor, if
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#' `FALSE` (the default) create a regular (nominal) factor.
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#' @param levels How to create the levels of the generated factor:
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#'
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#' * "default": uses labels where available, otherwise the values.
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#' Labels are sorted by value.
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#' * "both": like "default", but pastes together the level and value
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#' * "label": use only the labels; unlabelled values become `NA`
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#' * "values": use only the values
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#' @rdname as_factor
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#' @export
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as_factor.haven_labelled <- function(x, ...) {
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labels <- get_attr(x)
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x <- haven::as_factor(x, ...)
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set_attr(x, labels[-match("class", names(labels))])
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as_factor.haven_labelled <- function(x, levels = c("default", "labels", "values", "both"),
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ordered = FALSE, ...) {
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labels_all <- get_attr(x)
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levels <- match.arg(levels)
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label <- attr(x, "label", exact = TRUE)
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labels <- attr(x, "labels")
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if (levels %in% c("default", "both")) {
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if (levels == "both") {
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names(labels) <- paste0("[", labels, "] ", names(labels))
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}
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# Replace each value with its label
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vals <- unique(vctrs::vec_data(x))
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levs <- replace_with(vals, unname(labels), names(labels))
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# Ensure all labels are preserved
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levs <- sort(c(stats::setNames(vals, levs), labels), na.last = TRUE)
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levs <- unique(names(levs))
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x <- replace_with(vctrs::vec_data(x), unname(labels), names(labels))
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x <- factor(x, levels = levs, ordered = ordered)
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} else if (levels == "labels") {
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levs <- unname(labels)
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labs <- names(labels)
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x <- replace_with(vctrs::vec_data(x), levs, labs)
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x <- factor(x, unique(labs), ordered = ordered)
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} else if (levels == "values") {
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if (all(x %in% labels)) {
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levels <- unname(labels)
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} else {
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levels <- sort(unique(vctrs::vec_data(x)))
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}
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x <- factor(vctrs::vec_data(x), levels, ordered = ordered)
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}
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x <- structure(x, label = label)
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set_attr(x, labels_all, overwrite = FALSE)
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}
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#' @export
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#' @rdname as_factor
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as_factor.labelled <- as_factor.haven_labelled
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replace_with <- function(x, from, to) {
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stopifnot(length(from) == length(to))
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out <- x
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# First replace regular values
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matches <- match(x, from, incomparables = NA)
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if (anyNA(matches)) {
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out[!is.na(matches)] <- to[matches[!is.na(matches)]]
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} else {
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out <- to[matches]
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}
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# Then tagged missing values
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tagged <- haven::is_tagged_na(x)
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if (!any(tagged)) {
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return(out)
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}
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matches <- match(haven::na_tag(x), haven::na_tag(from), incomparables = NA)
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# Could possibly be faster to use anyNA(matches)
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out[!is.na(matches)] <- to[matches[!is.na(matches)]]
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out
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}
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#' Get named vector of factor levels and values
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@ -87,11 +162,13 @@ as_factor.labelled <- as_factor.haven_labelled
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#' structure(c(1, 2, 3, 2, 10, 9),
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#' labels = c(Unknown = 9, Refused = 10),
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#' class = "haven_labelled"
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#' ) |> as_factor() |> named_levels()
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#' ) |>
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#' as_factor() |>
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#' named_levels()
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#' }
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named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
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named_levels <- function(data, label = "labels", na.label = NULL, na.value = 99) {
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stopifnot(is.factor(data))
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if (!is.null(na.label)){
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if (!is.null(na.label)) {
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attrs <- attributes(data)
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lvls <- as.character(data)
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lvls[is.na(lvls)] <- na.label
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@ -101,17 +178,24 @@ named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
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lbls <- data.frame(
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name = lvls,
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value = vals
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) |> unique() |>
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) |>
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unique() |>
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(\(d){
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stats::setNames(d$value, d$name)
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})() |>
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sort()
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data <- do.call(structure,
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c(list(.Data=match(vals,lbls)),
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attrs[-match("levels", names(attrs))],
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list(levels=names(lbls),
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labels=lbls)))
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data <- do.call(
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structure,
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c(
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list(.Data = match(vals, lbls)),
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attrs[-match("levels", names(attrs))],
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list(
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levels = names(lbls),
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labels = lbls
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)
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)
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)
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}
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d <- data.frame(
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@ -123,7 +207,12 @@ named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
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## Applying labels
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attr_l <- attr(x = data, which = label, exact = TRUE)
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if (length(attr_l) != 0) {
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d$value[match(names(attr_l), d$name)] <- unname(attr_l)
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if (all(names(attr_l) %in% d$name)){
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d$value[match(names(attr_l), d$name)] <- unname(attr_l)
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}else {
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d$name[match(attr_l, d$name)] <- names(attr_l)
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d$value[match(names(attr_l), d$name)] <- unname(attr_l)
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}
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}
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out <- stats::setNames(d$value, d$name)
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@ -147,9 +236,9 @@ named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
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#' @export
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#'
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#' @examples
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#' \dontrun{
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#' c(1, 4, 3, "A", 7, 8, 1) |>
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#' as_factor() |> fct2num()
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#' as_factor() |>
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#' fct2num()
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#'
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#' structure(c(1, 2, 3, 2, 10, 9),
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#' labels = c(Unknown = 9, Refused = 10),
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@ -159,14 +248,44 @@ named_levels <- function(data, label = "labels",na.label=NULL, na.value=99) {
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#' fct2num()
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#'
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#' structure(c(1, 2, 3, 2, 10, 9),
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#' labels = c(Unknown = 9, Refused = 10)
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#' labels = c(Unknown = 9, Refused = 10),
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#' class = "labelled"
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#' ) |>
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#' as_factor() |>
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#' fct2num()
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#' }
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#'
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#' # Outlier with labels, but no class of origin, handled like numeric vector
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#' # structure(c(1, 2, 3, 2, 10, 9),
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#' # labels = c(Unknown = 9, Refused = 10)
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#' # ) |>
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#' # as_factor() |>
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#' # fct2num()
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#'
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#' v <- sample(6:19,20,TRUE) |> factor()
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#' dput(v)
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#' named_levels(v)
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#' fct2num(v)
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fct2num <- function(data) {
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stopifnot(is.factor(data))
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as.numeric(named_levels(data))[match(data, names(named_levels(data)))]
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if (is.character(named_levels(data))){
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values <- as.numeric(named_levels(data))
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} else {
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values <- named_levels(data)
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}
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out <- values[match(data, names(named_levels(data)))]
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## If no NA on numeric coercion, of original names, then return
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## original numeric names, else values
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if (possible_numeric(out)) {
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out <- as.numeric(names(out))
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}
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unname(out)
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}
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possible_numeric <- function(data){
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length(stats::na.omit(suppressWarnings(as.numeric(names(data))))) ==
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length(data)
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}
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#' Extract attribute. Returns NA if none
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@ -179,7 +298,7 @@ fct2num <- function(data) {
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#'
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#' @examples
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#' attr(mtcars$mpg, "label") <- "testing"
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#' do.call(c,sapply(mtcars, get_attr))
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#' do.call(c, sapply(mtcars, get_attr))
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#' \dontrun{
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#' mtcars |>
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#' numchar2fct(numeric.threshold = 6) |>
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@ -209,16 +328,22 @@ get_attr <- function(data, attr = NULL) {
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#' @return vector with attribute
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#' @export
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#'
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set_attr <- function(data, label, attr = NULL, overwrite=FALSE) {
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set_attr <- function(data, label, attr = NULL, overwrite = FALSE) {
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# browser()
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if (is.null(attr)) {
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## Has to be list...
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stopifnot(is.list(label))
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## ... with names
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stopifnot(length(label)==length(names(label)))
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if (!overwrite){
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## Has to be a named list
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## Will not fail, but just return original data
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if (!is.list(label) | length(label) != length(names(label))) {
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return(data)
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}
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## Only include named labels
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label <- label[!is.na(names(label))]
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if (!overwrite) {
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label <- label[!names(label) %in% names(attributes(data))]
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}
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attributes(data) <- c(attributes(data),label)
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attributes(data) <- c(attributes(data), label)
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} else {
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attr(data, attr) <- label
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}
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@ -251,4 +376,3 @@ haven_all_levels <- function(data) {
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}
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out
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}
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@ -5,6 +5,6 @@ account: agdamsbo
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server: shinyapps.io
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hostUrl: https://api.shinyapps.io/v1
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appId: 11351429
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bundleId: 9391508
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bundleId: 9391578
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url: https://agdamsbo.shinyapps.io/redcapcast/
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version: 1
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@ -2,6 +2,7 @@
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% Please edit documentation in R/as_factor.R
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\name{as_factor}
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\alias{as_factor}
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\alias{as_factor.factor}
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\alias{as_factor.logical}
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\alias{as_factor.numeric}
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\alias{as_factor.character}
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@ -11,20 +12,43 @@
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\usage{
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as_factor(x, ...)
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\method{as_factor}{factor}(x, ...)
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\method{as_factor}{logical}(x, ...)
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\method{as_factor}{numeric}(x, ...)
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\method{as_factor}{character}(x, ...)
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\method{as_factor}{haven_labelled}(x, ...)
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\method{as_factor}{haven_labelled}(
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x,
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levels = c("default", "labels", "values", "both"),
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ordered = FALSE,
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...
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)
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\method{as_factor}{labelled}(x, ...)
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\method{as_factor}{labelled}(
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x,
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levels = c("default", "labels", "values", "both"),
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ordered = FALSE,
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...
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)
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}
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\arguments{
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\item{x}{Object to coerce to a factor.}
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\item{...}{Other arguments passed down to method.}
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\item{levels}{How to create the levels of the generated factor:
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|
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* "default": uses labels where available, otherwise the values.
|
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Labels are sorted by value.
|
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* "both": like "default", but pastes together the level and value
|
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* "label": use only the labels; unlabelled values become `NA`
|
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* "values": use only the values}
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|
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\item{ordered}{If `TRUE` create an ordered (ordinal) factor, if
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`FALSE` (the default) create a regular (nominal) factor.}
|
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}
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\description{
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This extends [forcats::as_factor()] as well as [haven::as_factor()], by appending
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@ -33,15 +57,15 @@ ta loss in case of rich formatted and labelled data.
|
||||
}
|
||||
\details{
|
||||
Please refer to parent functions for extended documentation.
|
||||
To avoid redundancy calls and errors, functions are copy-pasted here
|
||||
}
|
||||
\examples{
|
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# will preserve all attributes but class
|
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\dontrun{
|
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# will preserve all attributes
|
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c(1, 4, 3, "A", 7, 8, 1) |> as_factor()
|
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structure(c(1, 2, 3, 2, 10, 9),
|
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labels = c(Unknown = 9, Refused = 10)
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) |>
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as_factor()
|
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as_factor() |> dput()
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|
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structure(c(1, 2, 3, 2, 10, 9),
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labels = c(Unknown = 9, Refused = 10),
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@ -49,4 +73,3 @@ structure(c(1, 2, 3, 2, 10, 9),
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) |>
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as_factor()
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}
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}
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@ -16,9 +16,9 @@ numeric vector
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Allows conversion of factor to numeric values preserving original levels
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}
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\examples{
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\dontrun{
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c(1, 4, 3, "A", 7, 8, 1) |>
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as_factor() |> fct2num()
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as_factor() |>
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fct2num()
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|
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structure(c(1, 2, 3, 2, 10, 9),
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labels = c(Unknown = 9, Refused = 10),
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@ -28,9 +28,21 @@ structure(c(1, 2, 3, 2, 10, 9),
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fct2num()
|
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|
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structure(c(1, 2, 3, 2, 10, 9),
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labels = c(Unknown = 9, Refused = 10)
|
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labels = c(Unknown = 9, Refused = 10),
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class = "labelled"
|
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) |>
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as_factor() |>
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fct2num()
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}
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|
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# Outlier with labels, but no class of origin, handled like numeric vector
|
||||
# structure(c(1, 2, 3, 2, 10, 9),
|
||||
# labels = c(Unknown = 9, Refused = 10)
|
||||
# ) |>
|
||||
# as_factor() |>
|
||||
# fct2num()
|
||||
|
||||
v <- sample(6:19,20,TRUE) |> factor()
|
||||
dput(v)
|
||||
named_levels(v)
|
||||
fct2num(v)
|
||||
}
|
||||
|
||||
@ -19,7 +19,7 @@ Extract attribute. Returns NA if none
|
||||
}
|
||||
\examples{
|
||||
attr(mtcars$mpg, "label") <- "testing"
|
||||
do.call(c,sapply(mtcars, get_attr))
|
||||
do.call(c, sapply(mtcars, get_attr))
|
||||
\dontrun{
|
||||
mtcars |>
|
||||
numchar2fct(numeric.threshold = 6) |>
|
||||
|
||||
@ -27,6 +27,8 @@ Get named vector of factor levels and values
|
||||
structure(c(1, 2, 3, 2, 10, 9),
|
||||
labels = c(Unknown = 9, Refused = 10),
|
||||
class = "haven_labelled"
|
||||
) |> as_factor() |> named_levels()
|
||||
) |>
|
||||
as_factor() |>
|
||||
named_levels()
|
||||
}
|
||||
}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user