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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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11
R/key_antimicrobials.R
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@ -30,7 +30,7 @@
#' (Key) Antimicrobials for First Weighted Isolates
#'
#' These functions can be used to determine first weighted isolates by considering the phenotype for isolate selection (see [first_isolate()]). Using a phenotype-based method to determine first isolates is more reliable than methods that disregard phenotypes.
#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically
#' @param x a [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank to determine automatically.
#' @param y,z [character] vectors to compare
#' @inheritParams first_isolate
#' @param universal names of **broad-spectrum** antimicrobial drugs, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antimicrobial drugs
@ -73,7 +73,6 @@
#' - Tetracycline
#' - Vancomycin
#'
#'
#' The default antimicrobial drugs used for **fungi** (set in `antifungal`) are:
#'
#' - Anidulafungin
@ -102,7 +101,7 @@
#'
#' \donttest{
#' if (require("dplyr")) {
#' # set key antibiotics to a new variable
#' # set key antimicrobials to a new variable
#' my_patients <- example_isolates %>%
#' mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`
#' mutate(
@ -192,7 +191,7 @@ key_antimicrobials <- function(x = NULL,
)
}
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
generate_antimicrobials_string(x[which(filter), c(universal, values), drop = FALSE])
}
if (is.null(universal)) {
@ -264,10 +263,10 @@ all_antimicrobials <- function(x = NULL,
sort = FALSE, fn = "all_antimicrobials"
)
generate_antimcrobials_string(x[, cols, drop = FALSE])
generate_antimicrobials_string(x[, cols, drop = FALSE])
}
generate_antimcrobials_string <- function(df) {
generate_antimicrobials_string <- function(df) {
if (NCOL(df) == 0) {
return(rep("", NROW(df)))
}