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make rsi work in more cases, documentation update

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dr. M.S. (Matthijs) Berends
2023-02-22 14:38:57 +01:00
parent 380cbec0e8
commit dad25302f2
87 changed files with 401 additions and 327 deletions
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10
data-raw/reproduction_of_antibiotics.R
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@ -188,7 +188,7 @@ abx2 <- abx2 %>%
abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
# Update Compound IDs and Trade Names ----
# Update Compound IDs and Synonyms ----
# vector with official names, returns vector with CIDs
get_CID <- function(ab) {
@ -307,6 +307,7 @@ get_synonyms <- function(CID, clean = TRUE) {
# get brand names from PubChem (3-4 min)
synonyms <- get_synonyms(CIDs)
synonyms.bak <- synonyms
# add existing ones (will be cleaned later)
for (i in seq_len(length(synonyms))) {
old <- antibiotics$synonyms[[i]]
@ -318,6 +319,13 @@ for (i in seq_len(length(synonyms))) {
antibiotics$synonyms <- synonyms
stop("remember to remove co-trimoxazole as synonyms from SXT (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]]
sulfa <- sulfa[!sulfa %in% cotrim]
antibiotics[which(antibiotics$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa
# now go to end of this file