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(v2.1.1.9094) fix antibiotics

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dr. M.S. (Matthijs) Berends
2024-10-10 16:38:20 +02:00
parent ef79d22daf
commit 94501371cd
21 changed files with 1390 additions and 440 deletions
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14
data-raw/reproduction_of_antibiotics.R
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@ -907,17 +907,19 @@ for (i in 1:nrow(antibiotics)) {
abb <- as.character(sort(unique(tolower(antibiotics[i, "abbreviations", drop = TRUE][[1]]))))
abb <- abb[abb != "" & abb %unlike% ":"]
syn <- as.character(sort(unique(tolower(unname(unlist(antibiotics[i, "synonyms", drop = TRUE]))))))
pharm_terms <- "(pa?ediatric|injection|oral|inhale|otic|sulfate|sulphate|sodium|base|anhydrous|anhydrate|syrup|natrium|hydrate|x?hcl|gsalt|vet[.]?)"
syn <- gsub("[^a-z]", "", syn)
syn <- gsub(" +", " ", syn)
pharm_terms <- "(pa?ediatric|injection|oral|inhale|otic|sulfate|sulphate|sodium|base|anhydrous|anhydrate|stearate|syrup|natrium|hydrate|x?hcl|gsalt|vet[.]?)"
syn <- gsub(paste0(" ", pharm_terms, "$"), "", syn)
syn <- gsub(paste0("^", pharm_terms, " "), "", syn)
syn <- gsub(" \\b[a-z]{1}\\.?[a-z]{1}\\.?$", "", syn, perl = TRUE)
syn <- trimws(syn)
syn <- gsub(" [a-z]{1,3}$", "", syn, perl = TRUE)
syn <- trimws(syn)
syn <- syn[syn != "" & syn %unlike% ":" & !syn %in% tolower(antibiotics$name)]
syn <- unique(syn)
if (antibiotics$ab[i] == "VAN") {
# special case
syn <- syn[syn %unlike% "^tei?ch?o"]
}
# special cases
if (antibiotics$ab[i] == "VAN") syn <- syn[syn %unlike% "^tei?ch?o"]
if (antibiotics$ab[i] == "CLR") syn <- syn[syn %unlike% "^ery"]
antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb) == 0, list(""), list(abb))
antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn) == 0, list(""), list(syn))
if ("loinc" %in% colnames(antibiotics)) {