P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 05:21:50 +02:00
Code Releases Activity

(v2.1.1.9190) antibiotics deprecation in antibiogram()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-09 10:41:11 +01:00
parent c7af397edf
commit a2c2be23c1
26 changed files with 203 additions and 180 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
R/zz_deprecated.R
View File

@ -40,22 +40,25 @@ NULL
#' @export
"antibiotics"
# REMEMBER to also remove the deprecated `antibiotics` argument in `antibiogram()`
#' @rdname AMR-deprecated
#' @export
ab_class <- function(...) {
deprecation_warning("ab_class", "amr_class")
deprecation_warning("ab_class", "amr_class", is_function = TRUE)
amr_class(...)
}
#' @rdname AMR-deprecated
#' @export
ab_selector <- function(...) {
deprecation_warning("ab_selector", "amr_selector")
deprecation_warning("ab_selector", "amr_selector", is_function = TRUE)
amr_selector(...)
}
## Helper function ----
deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_function = TRUE, is_dataset = FALSE) {
deprecation_warning <- function(old = NULL, new = NULL, fn = NULL, extra_msg = NULL, is_function = FALSE, is_dataset = FALSE, is_argument = FALSE) {
if (is.null(old)) {
warning_(extra_msg)
} else {
@ -68,22 +71,30 @@ deprecation_warning <- function(old = NULL, new = NULL, extra_msg = NULL, is_fun
type <- "function"
} else if (isTRUE(is_dataset)) {
type <- "dataset"
} else {
} else if (isTRUE(is_argument)) {
type <- "argument"
if (is.null(fn)) {
stop("Set 'fn' in deprecation_warning()")
}
} else {
stop("Set either 'is_function', 'is_dataset', or 'is_argument' to TRUE in deprecation_warning()")
}
warning_(
ifelse(is.null(new),
paste0("The `", old, "` ", type, " is no longer in use"),
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",
paste0("The `", old, "` ", type, " in `", fn, "()` has been renamed to `", new, "`: `", fn, "(", new, " = ...)`"),
paste0("The `", old, "` ", type, " has been replaced with `", new, "`")
)
)
),
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`."
" and will be removed in a future version, see `?AMR-deprecated`."
)
),
ifelse(!is.null(extra_msg),