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AMR
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unit test fix

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dr. M.S. (Matthijs) Berends 2024-04-24 11:42:43 +02:00
parent 3e5c7d45c6
commit 7f18e66c4e
1 changed files with 5 additions and 5 deletions
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R/ab.R
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@ -645,14 +645,14 @@ generalise_antibiotic_name <- function(x) {
x <- gsub("_(MIC|RSI|SIR|DIS[CK])$", "", x, perl = TRUE)
# remove disk concentrations, like LVX_NM -> LVX
x <- gsub("_[A-Z]{2}[0-9_.]{0,3}$", "", x, perl = TRUE)
# correct for 'high level' antibiotics
x <- gsub("([^A-Z0-9]+)?(HIGH(.?LEVEL)?|H[^A-Z0-9]?L)([^A-Z0-9]+)?", "-HIGH", x, perl = TRUE)
# remove part between brackets if that's followed by another string
x <- gsub("(.*)+ [(].*[)]", "\\1", x)
# keep only max 1 space
x <- trimws2(gsub(" +", " ", x, perl = TRUE))
# non-character, space or number should be a slash
x <- gsub("[^A-Z0-9 -]", "/", x, perl = TRUE)
x <- gsub("[^A-Z0-9 -)(]", "/", x, perl = TRUE)
# correct for 'high level' antibiotics
x <- gsub("([^A-Z0-9/ -]+)?(HIGH(.?LE?VE?L)?|[^A-Z0-9/]H[^A-Z0-9]?L)([^A-Z0-9 -]+)?", "-HIGH", x, perl = TRUE)
# remove part between brackets if that's followed by another string
x <- gsub("(.*)+ [(].*[)]", "\\1", x)
# spaces around non-characters must be removed: amox + clav -> amox/clav
x <- gsub("(.*[A-Z0-9]) ([^A-Z0-9].*)", "\\1\\2", x, perl = TRUE)
x <- gsub("(.*[^A-Z0-9]) ([A-Z0-9].*)", "\\1\\2", x, perl = TRUE)