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(v0.8.0.9010) mdro bug fix

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dr. M.S. (Matthijs) Berends
2019-11-04 11:35:34 +01:00
parent 0bb531f3e0
commit 9060233953
12 changed files with 29 additions and 19 deletions
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8
R/mdro.R
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@ -48,7 +48,7 @@
#' \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`)")
# set these -1s to NA