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(v3.0.1.9062) Fix older R versions

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dr. M.S. (Matthijs) Berends
2026-06-24 10:19:15 +02:00
parent 0c1709c999
commit ab38fb911d
6 changed files with 26 additions and 20 deletions
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12
R/mdro.R
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@@ -1511,8 +1511,8 @@ mdro <- function(x = NULL,
fluoroquinolones <- c(CIP, NOR, LVX) # note 5: ciprofloxacin or norfloxacin or levofloxacin
carbapenems <- carbapenems[!is.na(carbapenems)]
carbapenems_without_imipenem <- carbapenems[carbapenems != IPM]
amino <- AMX %or% AMP
third <- CAZ %or% CTX
amino <- AMX %or_if_na% AMP
third <- CAZ %or_if_na% CTX
ESBLs <- c(amino, third)
ESBLs <- ESBLs[!is.na(ESBLs)]
if (length(ESBLs) != 2) {
@@ -1524,7 +1524,7 @@ mdro <- function(x = NULL,
trans_tbl(
2, # positive, unconfirmed
rows = which(x$order == "Enterobacterales" & col_values(x, ESBLs[1]) == "R" & col_values(x, ESBLs[2]) == "R" & is.na(esbl)),
cols = c(AMX %or% AMP, cephalosporins_3rd),
cols = c(AMX %or_if_na% AMP, cephalosporins_3rd),
any_all = "all",
reason = "Enterobacterales: potential ESBL"
)
@@ -1634,7 +1634,7 @@ mdro <- function(x = NULL,
trans_tbl(
3,
rows = which(x$genus == "Enterococcus" & x$species == "faecium"),
cols = c(PEN %or% AMX %or% AMP, VAN),
cols = c(PEN %or_if_na% AMX %or_if_na% AMP, VAN),
any_all = "all",
reason = "E. faecium: vancomycin + penicillin group"
)
@@ -1677,8 +1677,8 @@ mdro <- function(x = NULL,
aminoglycosides <- aminoglycosides[!is.na(aminoglycosides)]
fluoroquinolones <- fluoroquinolones[!is.na(fluoroquinolones)]
carbapenems <- carbapenems[!is.na(carbapenems)]
amino <- AMX %or% AMP
third <- CAZ %or% CTX
amino <- AMX %or_if_na% AMP
third <- CAZ %or_if_na% CTX
ESBLs <- c(amino, third)
ESBLs <- ESBLs[!is.na(ESBLs)]
if (length(ESBLs) != 2) {