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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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6
R/key_antimicrobials.R
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@ -37,7 +37,7 @@
#' @param gram_negative Names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
#' @param gram_positive Names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
#' @param antifungal Names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs.
#' @param only_sir_columns A [logical] to indicate whether only columns must be included 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()].
#' @param ... Ignored, only in place to allow future extensions.
#' @details
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
@ -134,7 +134,7 @@ key_antimicrobials <- function(x = NULL,
"anidulafungin", "caspofungin", "fluconazole",
"miconazole", "nystatin", "voriconazole"
),
only_sir_columns = FALSE,
only_sir_columns = any(is.sir(x)),
...) {
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@ -246,7 +246,7 @@ key_antimicrobials <- function(x = NULL,
#' @rdname key_antimicrobials
#' @export
all_antimicrobials <- function(x = NULL,
only_sir_columns = FALSE,
only_sir_columns = any(is.sir(x)),
...) {
if (is_null_or_grouped_tbl(x)) {
# when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)