mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 13:01:59 +02:00
(v0.9.0.9023) EUCAST 2020 guidelines
This commit is contained in:
4
R/mdro.R
4
R/mdro.R
@ -90,6 +90,8 @@ mdro <- function(x,
|
||||
verbose = FALSE,
|
||||
...) {
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
if (verbose == TRUE & interactive()) {
|
||||
txt <- paste0("WARNING: In Verbose mode, the mdro() function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.",
|
||||
"\n\nThis may overwrite your existing data if you use e.g.:",
|
||||
@ -147,7 +149,7 @@ mdro <- function(x,
|
||||
if (is.null(col_mo) & guideline$code == "tb") {
|
||||
message(blue("NOTE: No column found as input for `col_mo`,",
|
||||
bold("assuming all records contain", italic("Mycobacterium tuberculosis.\n"))))
|
||||
x$mo <- AMR::as.mo("Mycobacterium tuberculosis")
|
||||
x$mo <- as.mo("Mycobacterium tuberculosis")
|
||||
col_mo <- "mo"
|
||||
}
|
||||
if (is.null(col_mo)) {
|
||||
|
Reference in New Issue
Block a user