* Support for a new MDRO guideline: Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012).
@ -18,6 +18,7 @@
### Other
* Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request
#' \item{Everything else:\cr Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests}
#' }
#' @rdname mdro
#' @importFrom dplyr %>% filter_all
#' @importFrom dplyr %>% filter_at vars all_vars pull
#' @importFrom crayon blue bold italic
#' @importFrom cleaner percentage
#' @export
@ -474,8 +474,8 @@ mdro <- function(x,
function(row,group_tbl=lst){
sum(sapply(group_tbl,
function(group){
any(x[row,group[!is.na(group)]]=="R")|
any(x[row,group[!is.na(group)]]=="I")
any(x[row,group[!is.na(group)]]=="R",na.rm=TRUE)|
any(x[row,group[!is.na(group)]]=="I",na.rm=TRUE)
}),
na.rm=TRUE)
})
@ -975,7 +975,7 @@ mdro <- function(x,
# Results ----
if (guideline$code=="cmi2012"){
if (any(x$MDRO==-1)){
if (any(x$MDRO==-1,na.rm=TRUE)){
warning("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes)," (set with `pct_required_classes`)")
