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completely updated antibiotics

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-30 14:31:45 +01:00
parent 3d9faf89cf
commit d40e0ef20b
60 changed files with 102028 additions and 95116 deletions
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59
data-raw/reproduction_of_antibiotics.R
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@ -187,12 +187,14 @@ abx2 <- abx2 %>%
abx2$abbr <- lapply(as.list(abx2$abbr), function(x) unlist(strsplit(x, "|", fixed = TRUE)))
# Update Compound IDs and Trade Names ----
# vector with official names, returns vector with CIDs
get_CID <- function(ab) {
CID <- rep(NA_integer_, length(ab))
p <- progress_ticker(n = length(ab), min_time = 0)
for (i in 1:length(ab)) {
p$tick()$print()
p$tick()
CID[i] <- tryCatch(
data.table::fread(paste0(
@ -236,18 +238,20 @@ get_CID <- function(ab) {
CID
}
# get CIDs (2-3 min)
CIDs <- get_CID(abx2$name)
# get CIDs (4-5 min)
CIDs <- get_CID(antibiotics$name)
# take missing from previously found CIDs
CIDs[is.na(CIDs) & !is.na(antibiotics$cid)] <- antibiotics$cid[is.na(CIDs) & !is.na(antibiotics$cid)]
# These could not be found:
abx2[is.na(CIDs), ] %>% View()
antibiotics[is.na(CIDs), ] %>% View()
# returns list with synonyms (brand names), with CIDs as names
get_synonyms <- function(CID, clean = TRUE) {
synonyms <- rep(NA_character_, length(CID))
# p <- progress_ticker(n = length(CID), min_time = 0)
p <- progress_ticker(n = length(CID), min_time = 0)
for (i in 1:length(CID)) {
# p$tick()$print()
p$tick()
synonyms_txt <- ""
@ -284,7 +288,7 @@ get_synonyms <- function(CID, clean = TRUE) {
synonyms_txt <- gsub("Co-", "Co", synonyms_txt, fixed = TRUE)
# only length 6 to 20 and no txt with reading marks or numbers and must start with capital letter (= brand)
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(6:20) &
!grepl("[-&{},_0-9/]", synonyms_txt) &
!grepl("[-&{},_0-9/:]", synonyms_txt) &
grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)]
synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
}
@ -295,18 +299,24 @@ get_synonyms <- function(CID, clean = TRUE) {
synonyms
}
# get brand names from PubChem (2-3 min)
# get brand names from PubChem (3-4 min)
synonyms <- get_synonyms(CIDs)
synonyms <- lapply(
synonyms,
function(x) {
if (length(x) == 0 | all(is.na(x))) {
""
} else {
x
}
synonyms.bak <- synonyms
# add existing ones (will be cleaned later)
for (i in seq_len(length(synonyms))) {
old <- antibiotics$synonyms[[i]]
if (old %like% "^c[()]") {
old <- eval(parse(text = old))
}
)
synonyms[[i]] <- c(synonyms[[i]], old)
}
antibiotics$synonyms <- synonyms
# now go to end of this file
# -----
# add them to data set
antibiotics <- abx2 %>%
@ -830,13 +840,16 @@ antibiotics <- dplyr::arrange(antibiotics, name)
# make all abbreviations and synonyms lower case, unique and alphabetically sorted ----
for (i in 1:nrow(antibiotics)) {
abb <- as.character(sort(unique(tolower(antibiotics[i, "abbreviations"][[1]]))))
syn <- as.character(sort(unique(tolower(antibiotics[i, "synonyms"][[1]]))))
antibiotics[i, "abbreviations"][[1]] <- ifelse(length(abb[!abb == ""]) == 0, list(""), list(abb))
antibiotics[i, "synonyms"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(syn))
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% ":"]
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)) {
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc"][[1]]))))
antibiotics[i, "loinc"][[1]] <- ifelse(length(syn[!syn == ""]) == 0, list(""), list(loinc))
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc", drop = TRUE][[1]]))))
loinc <- loinc[loinc != ""]
antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
}
}