From 7f18e66c4e4686d1f4783a763f2b90975ea2d556 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 24 Apr 2024 11:42:43 +0200 Subject: [PATCH] unit test fix --- R/ab.R | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/R/ab.R b/R/ab.R index 4898a549..ed7ce5e6 100755 --- a/R/ab.R +++ b/R/ab.R @@ -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)