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(v0.9.0.9023) EUCAST 2020 guidelines

This commit is contained in:
2020-02-14 19:54:13 +01:00
parent 5a98e6b777
commit 9b8b02960e
43 changed files with 16588 additions and 14564 deletions

View File

@ -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)) {