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(v2.1.1.9093) New brand names

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dr. M.S. (Matthijs) Berends
2024-10-06 22:30:52 +02:00
parent c588902f4c
commit ef79d22daf
16 changed files with 456 additions and 424 deletions
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28
data-raw/reproduction_of_antibiotics.R
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@ -276,7 +276,10 @@ get_synonyms <- function(CID, clean = TRUE) {
)[[1]],
error = function(e) NA_character_
)
# include the current CID of course
all_cids <- unique(c(CID[i], similar_cids))
# but leave out all CIDs that we have in our antibiotics dataset to prevent duplication
all_cids <- all_cids[!all_cids %in% antibiotics$cid[!is.na(antibiotics$cid)]]
# for each one, we are getting the synonyms
current_syns <- character(0)
for (j in seq_len(length(all_cids))) {
@ -309,7 +312,7 @@ get_synonyms <- function(CID, clean = TRUE) {
))
synonyms_txt <- gsub("Co-", "Co", synonyms_txt, fixed = TRUE)
synonyms_txt <- gsub(" ?(mono)?sodium ?", "", ignore.case = TRUE, synonyms_txt)
synonyms_txt <- gsub(" ?injection ?", "", ignore.case = TRUE, synonyms_txt)
synonyms_txt <- gsub(" ?(injection|pediatric) ?", "", ignore.case = TRUE, synonyms_txt)
# only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand)
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(5:20) &
!grepl("[-&{},_0-9/:]", synonyms_txt) &
@ -330,14 +333,12 @@ get_synonyms <- function(CID, clean = TRUE) {
# get brand names from PubChem (3-4 min)
synonyms <- get_synonyms(CIDs)
synonyms.bak <- synonyms
synonyms <- synonyms.bak
# add existing ones (will be cleaned later)
for (i in seq_len(length(synonyms))) {
old <- antibiotics$synonyms[[i]]
if (old %like% "^c[()]") {
old <- eval(parse(text = old))
}
synonyms[[i]] <- c(synonyms[[i]], old)
old <- unname(unlist(AMR::antibiotics[i, "synonyms", drop = TRUE]))
synonyms[[i]] <- c(unname(synonyms[[i]]), old)
}
antibiotics$synonyms <- synonyms
@ -345,6 +346,7 @@ antibiotics$synonyms <- synonyms
stop("remember to remove co-trimoxazole as synonyms from SMX (Sulfamethoxazole), so it only exists in SXT!")
sulfa <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms", drop = TRUE][[1]]
cotrim <- antibiotics[which(antibiotics$ab == "SXT"), "synonyms", drop = TRUE][[1]]
# 2024-10-06 not the case anymore, no overlapping names: sulfa[sulfa %in% cotrim]
sulfa <- sulfa[!sulfa %in% cotrim]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa
@ -904,8 +906,18 @@ antibiotics <- dplyr::arrange(antibiotics, name)
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(antibiotics[i, "synonyms", drop = TRUE][[1]]))))
syn <- syn[syn != "" & syn %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(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 <- 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"]
}
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)) {