P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 22:21:52 +02:00
Code Releases Activity

(v2.1.1.9285) mdro fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-05-21 16:51:40 +02:00
parent 8d2c5afab6
commit 80f08f91da
4 changed files with 19 additions and 11 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
R/mdro.R
View File

@ -499,10 +499,11 @@ mdro <- function(x = NULL,
if (!"AMP" %in% names(cols_ab) && "AMX" %in% names(cols_ab)) {
# ampicillin column is missing, but amoxicillin is available
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.")
message_("Using column '", cols_ab[names(cols_ab) == "AMX"], "' as input for ampicillin since many MDRO rules depend on it.", add_fn = font_red)
}
cols_ab <- c(cols_ab, c(AMP = unname(cols_ab[names(cols_ab) == "AMX"])))
}
cols_ab <- cols_ab[!duplicated(cols_ab)]
# nolint start
AMC <- cols_ab["AMC"]
@ -1607,20 +1608,20 @@ mdro <- function(x = NULL,
reason = "E. faecium: vanA/vanB gene + penicillin group"
)
# Staphylococcus aureus
# Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
trans_tbl(
2,
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (is.na(mecA) | is.na(mecC))),
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
any_all = "any",
reason = "S. aureus: potential MRSA"
reason = "S. aureus complex: potential MRSA"
)
trans_tbl(
3,
rows = which(x$genus == "Staphylococcus" & x$species == "aureus" & (mecA == TRUE | mecC == TRUE)),
rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
cols = "any",
any_all = "any",
reason = "S. aureus: mecA/mecC gene"
reason = "S. aureus complex: mecA/mecC gene"
)
# Candida auris