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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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6
R/ab.R
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@ -88,9 +88,9 @@
#' \donttest{
#' if (require("dplyr")) {
#'
#' # you can quickly rename 'rsi' columns using set_ab_names() with dplyr:
#' # you can quickly rename 'sir' columns using set_ab_names() with dplyr:
#' example_isolates %>%
#' set_ab_names(where(is.rsi), property = "atc")
#' set_ab_names(where(is.sir), property = "atc")
#' }
#' }
as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
@ -632,7 +632,7 @@ rep.ab <- function(x, ...) {
generalise_antibiotic_name <- function(x) {
x <- toupper(x)
# remove suffices
x <- gsub("_(MIC|RSI|DIS[CK])$", "", x, perl = TRUE)
x <- gsub("_(MIC|RSI|SIR|DIS[CK])$", "", x, perl = TRUE)
# remove disk concentrations, like LVX_NM -> LVX
x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
# remove part between brackets if that's followed by another string