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(v2.1.1.9254) fix antimicrobial synonyms

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dr. M.S. (Matthijs) Berends
2025-04-26 16:23:14 +02:00
parent 4e7fca3b38
commit 92316d5ddc
15 changed files with 114 additions and 74 deletions
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13
data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R
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@ -1028,6 +1028,17 @@ antimicrobials <- dplyr::arrange(antimicrobials, name)
# REFER TO data-raw/loinc.R FOR ADDING LOINC CODES
# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
transform_syn <- function(x) {
x <- gsub("ph", "(ph|f)", x)
x <- gsub("th", "(th|t)", x)
x <- gsub("ae", "(ae|e)", x)
x <- gsub("oe", "(oe|e)", x)
x <- gsub("ck", "(ck|k)", x)
x <- gsub("c", "(c|k|s)", x)
x <- gsub("y", "(y|i)", x)
x <- gsub("z", "(z|s)", x)
x
}
for (i in 1:nrow(antimicrobials)) {
atc <- as.character(sort(unique(toupper(antimicrobials[i, "atc", drop = TRUE][[1]]))))
atc <- atc[atc != "" & atc %unlike% ":"]
@ -1043,6 +1054,8 @@ for (i in 1:nrow(antimicrobials)) {
syn <- gsub(" [a-z]{1,3}$", "", syn, perl = TRUE)
syn <- trimws(syn)
syn <- syn[syn != "" & syn %unlike% ":" & !syn %in% tolower(antimicrobials$name)]
# remove synonyms that are names in the data set
syn <- syn[!sapply(syn, function(s) any(grepl(transform_syn(s), antimicrobials$name)))]
syn <- unique(syn)
# special cases
if (antimicrobials$ab[i] == "VAN") syn <- syn[syn %unlike% "^tei?ch?o"]