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(v2.1.1.9217) allow + in amr selectors

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dr. M.S. (Matthijs) Berends
2025-03-18 16:35:22 +01:00
parent 8d8444c607
commit 4dc4398ad1
23 changed files with 543 additions and 440 deletions
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34
data-raw/reproduction_of_antimicrobials.R
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@@ -263,6 +263,8 @@ get_synonyms <- function(CID, clean = TRUE) {
next
}
all_cids <- CID[i]
# we will now get the closest compounds with a 96% threshold
similar_cids <- tryCatch(
data.table::fread(
@@ -276,10 +278,10 @@ 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 antimicrobials dataset to prevent duplication
all_cids <- all_cids[!all_cids %in% antimicrobials$cid[!is.na(antimicrobials$cid)]]
# leave out all CIDs that we have in our antimicrobials dataset to prevent duplication
similar_cids <- similar_cids[!similar_cids %in% antimicrobials$cid[!is.na(antimicrobials$cid)]]
all_cids <- unique(c(all_cids, similar_cids))
# for each one, we are getting the synonyms
current_syns <- character(0)
for (j in seq_len(length(all_cids))) {
@@ -312,14 +314,18 @@ 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(" ?HCl ?", "", 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 <- gsub("[^a-z]+$", "", ignore.case = TRUE, synonyms_txt)
# only length 5 to 20 and lower-case names starting with a capital letter
synonyms_txt <- synonyms_txt[nchar(synonyms_txt) %in% c(5:20) &
!grepl("[-&{},_0-9/:]", synonyms_txt) &
grepl("^[A-Z]", synonyms_txt, ignore.case = FALSE)]
grepl("^[A-Z][a-z]+$", synonyms_txt, ignore.case = FALSE)]
synonyms_txt <- unlist(strsplit(synonyms_txt, ";", fixed = TRUE))
}
# synonyms must not be set for other agents, so remove the duplicates
synonyms_txt <- synonyms_txt[!synonyms_txt %in% unlist(synonyms)]
current_syns <- c(current_syns, synonyms_txt)
}
@@ -335,20 +341,14 @@ 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 <- unname(unlist(AMR::antimicrobials[i, "synonyms", drop = TRUE]))
synonyms[[i]] <- c(unname(synonyms[[i]]), old)
}
antimicrobials$synonyms <- synonyms
stop("remember to remove co-trimoxazole as synonyms from SMX (Sulfamethoxazole), so it only exists in SXT!")
sulfa <- antimicrobials[which(antimicrobials$ab == "SMX"), "synonyms", drop = TRUE][[1]]
add_to_cotrim <- sulfa[sulfa %unlike% "^[s-z]"]
cotrim <- antimicrobials[which(antimicrobials$ab == "SXT"), "synonyms", drop = TRUE][[1]]
# 2024-10-06 not the case anymore, no overlapping names: sulfa[sulfa %in% cotrim]
sulfa <- sulfa[!sulfa %in% cotrim]
antimicrobials[which(antimicrobials$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa
antimicrobials[which(antimicrobials$ab == "SMX"), "synonyms"][[1]][[1]] <- sulfa[!sulfa %in% add_to_cotrim]
antimicrobials[which(antimicrobials$ab == "SXT"), "synonyms"][[1]][[1]] <- c(cotrim, add_to_cotrim)
# now go to end of this file
@@ -791,7 +791,7 @@ antimicrobials <- antimicrobials |>
bind_rows(
antimicrobials |>
filter(ab == "EFF") |>
mutate(ab = "BTL-S",
mutate(ab = "BLA-S",
name = paste("Beta-lactamase", "screening test"),
cid = NA_real_,
atc = list(character(0)),