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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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24
R/zz_deprecated.R
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@ -29,12 +29,16 @@
#' Deprecated Functions
#'
#' These functions are so-called '[Deprecated]'. **They will be removed in a future version of this package.** Using these functions will give a warning with the name of the function it has been replaced by (if there is one).
#' These objects are so-called '[Deprecated]'. **They will be removed in a future version of this package.** Using these will give a warning with the name of the alternative object it has been replaced by (if there is one).
#' @keywords internal
#' @name AMR-deprecated
#' @rdname AMR-deprecated
NULL
#' @rdname AMR-deprecated
#' @export
"antibiotics"
#' @rdname AMR-deprecated
#' @export
ab_class <- function(...) {
@ -50,7 +54,7 @@ ab_selector <- function(...) {
}
deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE) {
deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE, is_dataset = FALSE) {
if (is.null(old)) {
warning_(extra_msg)
} else {
@ -61,17 +65,25 @@ deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_fun
old <- paste0(old, "()")
new <- paste0(new, "()")
type <- "function"
} else if (isTRUE(is_dataset)) {
type <- "dataset"
} else {
type <- "argument"
}
warning_(
ifelse(is.null(new),
paste0("The `", old, "` ", type, " is no longer in use"),
paste0("The `", old, "` ", type, " has been replaced with `", new, "` and will be removed in a future version")
ifelse(type == "dataset",
paste0("The `", old, "` ", type, " has been renamed to `", new, "`"),
paste0("The `", old, "` ", type, " has been replaced with `", new, "` and will be removed in a future version")
)
),
ifelse(type == "argument",
". While the old argument still works, it will be removed in a future version, so please update your code.",
", see `?AMR-deprecated`."
ifelse(type == "dataset",
". The old name will be removed in future version, so please update your code.",
ifelse(type == "argument",
". While the old argument still works, it will be removed in a future version, so please update your code.",
", see `?AMR-deprecated`."
)
),
ifelse(!is.null(extra_msg),
paste0(" ", extra_msg),