P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 17:02:03 +02:00
Code Releases Activity

(v2.1.1.9123) add EFF code to antibiotics data set

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-01-15 16:14:09 +01:00
parent 2e31ec19c3
commit 08ddbaa930
32 changed files with 522 additions and 461 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
R/ab.R
View File

@ -687,3 +687,30 @@ get_translate_ab <- function(translate_ab) {
translate_ab
}
}
create_AB_AV_lookup <- function(df) {
new_df <- df
new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
if ("abbreviations" %in% colnames(df)) {
new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
}
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
new_df$generalised_all <- unname(lapply(
as.list(as.data.frame(
t(new_df[,
c(
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
colnames(new_df)[colnames(new_df) %like% "generalised"]
),
drop = FALSE
]),
stringsAsFactors = FALSE
)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}
))
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
}