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(v0.8.0.9001) guideline text on as.rsi()

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dr. M.S. (Matthijs) Berends
2019-10-21 14:12:28 +02:00
parent 1b8e2366f7
commit 666126cd5e
11 changed files with 51 additions and 16 deletions
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25
R/rsi.R
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@ -254,8 +254,28 @@ exec_as.rsi <- function(method, x, mo, ab, guideline) {
class = c("rsi", "ordered", "factor"))
}
get_guideline <- function(guideline) {
guideline_param <- toupper(guideline)
if (guideline_param %in% c("CLSI", "EUCAST")) {
guideline_param <- AMR::rsi_translation %>%
filter(guideline %like% guideline_param) %>%
pull(guideline) %>%
sort() %>%
rev() %>%
.[1]
}
if (!guideline_param %in% AMR::rsi_translation$guideline) {
stop(paste0("invalid guideline: '", guideline,
"'.\nValid guidelines are: ", paste0("'", rev(sort(unique(AMR::rsi_translation$guideline))), "'", collapse = ", ")),
call. = FALSE)
}
guideline_param
}
#' @rdname as.rsi
#' @importFrom crayon red blue
#' @importFrom crayon red blue bold
#' @export
as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
x <- x
@ -273,6 +293,9 @@ as.rsi.data.frame <- function(x, col_mo = NULL, guideline = "EUCAST", ...) {
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
guideline <- get_guideline(guideline)
message(blue("Interpreting using guideline", bold(guideline)))
# transform all MICs
ab_cols <- colnames(x)[sapply(x, is.mic)]