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make rsi
work in more cases, documentation update
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@ -188,7 +188,7 @@ abx2 <- abx2 %>%
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abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
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# Update Compound IDs and Trade Names ----
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# Update Compound IDs and Synonyms ----
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# vector with official names, returns vector with CIDs
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get_CID <- function(ab) {
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@ -307,6 +307,7 @@ get_synonyms <- function(CID, clean = TRUE) {
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# get brand names from PubChem (3-4 min)
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synonyms <- get_synonyms(CIDs)
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synonyms.bak <- synonyms
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# add existing ones (will be cleaned later)
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for (i in seq_len(length(synonyms))) {
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old <- antibiotics$synonyms[[i]]
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@ -318,6 +319,13 @@ for (i in seq_len(length(synonyms))) {
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antibiotics$synonyms <- synonyms
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stop("remember to remove co-trimoxazole as synonyms from SXT (Sulfamethoxazole), so it only exists in SXT!")
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sulfa <- antibiotics[which(antibiotics$ab == "SMX"), "synonyms", drop = TRUE][[1]]
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cotrim <- antibiotics[which(antibiotics$ab == "SXT"), "synonyms", drop = TRUE][[1]]
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sulfa <- sulfa[!sulfa %in% cotrim]
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antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa
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# now go to end of this file
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