P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 06:01:53 +02:00
Code Releases Activity

(v2.1.1.9288) mdro fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-06-01 15:35:04 +02:00
parent 5667ce3eae
commit 46f80b1378
5 changed files with 22 additions and 22 deletions
Download Patch File Download Diff File Expand all files Collapse all files

20
R/mdro.R
View File

@ -204,14 +204,14 @@ mdro <- function(x = NULL,
}
if (is.character(vanA)) {
meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
vanA <- x[[vanA]]
vanA <- x[[VanA]]
meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
} else if (length(vanA) == 1) {
vanA <- rep(vanA, NROW(x))
}
if (is.character(vanB)) {
meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
vanB <- x[[vanB]]
vanB <- x[[VanB]]
meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
} else if (length(vanB) == 1) {
vanB <- rep(vanB, NROW(x))
@ -1526,9 +1526,9 @@ mdro <- function(x = NULL,
)
trans_tbl(
3,
rows = which(x[[SXT]] == "R" &
(x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
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$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
cols = c(SXT, aminoglycosides, fluoroquinolones),
any_all = "any",
@ -1536,9 +1536,9 @@ mdro <- function(x = NULL,
)
trans_tbl(
3,
rows = which(x[[SXT]] == "R" &
x[[GEN]] == "R" &
(x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
rows = which(col_values(x, SXT) == "R" &
col_values(x, GEN) == "R" &
(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
paste(x$genus, x$species) == "Serratia marcescens"),
cols = c(SXT, aminoglycosides_serratia_marcescens, fluoroquinolones),
any_all = "any",
@ -1548,8 +1548,8 @@ mdro <- function(x = NULL,
# Acinetobacter baumannii-calcoaceticus complex
trans_tbl(
3,
rows = which((x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
(x[[CIP]] == "R" | x[[LVX]] == "R") &
rows = which((col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
(col_values(x, CIP) == "R" | col_values(x, LVX) == "R") &
x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
cols = c(aminoglycosides, CIP, LVX),
any_all = "any",