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v3.0.1

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dr. M.S. (Matthijs) Berends
2025-09-20 17:14:07 +01:00
parent 33fb1849eb
commit adee419f1c
9 changed files with 62 additions and 55 deletions
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R/mdro.R
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@@ -1499,12 +1499,13 @@ mdro <- function(x = NULL,
any_all = "any",
reason = "Enterobacterales: carbapenemase"
)
c.freundii_complex <- AMR::microorganisms.groups$mo_name[AMR::microorganisms.groups$mo_group_name == "Citrobacter freundii complex"]
trans_tbl(
3,
rows = which(col_values(x, SXT) == "R" &
(col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
(x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c(c.freundii_complex, "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
cols = c(SXT, aminoglycosides, fluoroquinolones),
any_all = "any",
reason = "Enterobacterales group II: aminoglycoside + fluoroquinolone + cotrimoxazol"