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(v2.1.1.9276) mdro() fix

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dr. M.S. (Matthijs) Berends
2025-05-15 10:39:48 +02:00
parent 48a59ee31a
commit 4b171745de
14 changed files with 64 additions and 94 deletions
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9
R/guess_ab_col.R
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@ -33,7 +33,7 @@
#' @param x A [data.frame].
#' @param search_string A text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`.
#' @param verbose A [logical] to indicate whether additional info should be printed.
#' @param only_sir_columns A [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be included that were transformed to class [sir][as.sir()] on beforehand. Defaults to `FALSE` if no columns of `x` have a class [sir][as.sir()].
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antimicrobials] data set for any column containing a name or code of that antibiotic.
#' @return A column name of `x`, or `NULL` when no result is found.
#' @export
@ -211,7 +211,7 @@ get_column_abx <- function(x,
newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
if (anyNA(newnames)) {
if (isTRUE(info)) {
message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
message_(paste0(font_yellow(font_bold(" WARNING: ")), "some columns returned `NA` for `as.ab()`"), as_note = FALSE)
}
warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
call = FALSE,
@ -254,7 +254,10 @@ get_column_abx <- function(x,
out <- out[order(names(out), out)]
}
dups <- FALSE
if (return_all == FALSE) {
dups <- names(out)[names(out) %in% names(out)[duplicated(names(out))]]
# only keep the first hits, no duplicates
duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
if (length(duplicates) > 0) {
@ -264,6 +267,8 @@ get_column_abx <- function(x,
if (isTRUE(info)) {
if (all_okay == TRUE) {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
} else if (!isFALSE(dups)) {
message_(paste0(font_yellow(font_bold(" WARNING: ")), "some results from `as.ab()` are duplicated: ", vector_and(dups, quotes = "`")), as_note = FALSE)
} else {
message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
}