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mirror of https://github.com/msberends/AMR.git synced 2025-07-13 02:32:07 +02:00

(v2.1.1.9186) replace antibiotics with antimicrobials!

This commit is contained in:
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions

View File

@ -50,15 +50,15 @@ loinc_df <- loinc_df %>%
filter(CLASS %in% c("DRUG/TOX", "ABXBACT")) %>%
mutate(name = generalise_antibiotic_name(COMPONENT), .before = 1)
# antibiotics
antibiotics$loinc <- as.list(rep(NA_character_, nrow(antibiotics)))
for (i in seq_len(nrow(antibiotics))) {
# antimicrobials
antimicrobials$loinc <- as.list(rep(NA_character_, nrow(antimicrobials)))
for (i in seq_len(nrow(antimicrobials))) {
message(i)
loinc_ab <- loinc_df %>%
filter(name %like% paste0("^", generalise_antibiotic_name(antibiotics$name[i]))) %>%
filter(name %like% paste0("^", generalise_antibiotic_name(antimicrobials$name[i]))) %>%
pull(LOINC_NUM)
if (length(loinc_ab) > 0) {
antibiotics$loinc[i] <- list(loinc_ab)
antimicrobials$loinc[i] <- list(loinc_ab)
}
}
@ -75,10 +75,10 @@ for (i in seq_len(nrow(antivirals))) {
}
# sort and fix for empty values
for (i in 1:nrow(antibiotics)) {
loinc <- as.character(sort(unique(tolower(antibiotics[i, "loinc", drop = TRUE][[1]]))))
for (i in 1:nrow(antimicrobials)) {
loinc <- as.character(sort(unique(tolower(antimicrobials[i, "loinc", drop = TRUE][[1]]))))
loinc <- loinc[loinc != ""]
antibiotics[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
}
for (i in 1:nrow(antivirals)) {
loinc <- as.character(sort(unique(tolower(antivirals[i, "loinc", drop = TRUE][[1]]))))
@ -86,17 +86,17 @@ for (i in 1:nrow(antivirals)) {
antivirals[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(""), list(loinc))
}
antibiotics <- dataset_UTF8_to_ASCII(as.data.frame(antibiotics, stringsAsFactors = FALSE))
antibiotics <- dplyr::arrange(antibiotics, name)
antimicrobials <- dataset_UTF8_to_ASCII(as.data.frame(antimicrobials, stringsAsFactors = FALSE))
antimicrobials <- dplyr::arrange(antimicrobials, name)
antivirals <- dataset_UTF8_to_ASCII(as.data.frame(antivirals, stringsAsFactors = FALSE))
antivirals <- dplyr::arrange(antivirals, name)
# remember to update R/aa_globals.R for the documentation
dim(antibiotics) # for R/data.R
usethis::use_data(antibiotics, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(antibiotics)
dim(antimicrobials) # for R/data.R
usethis::use_data(antimicrobials, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
rm(antimicrobials)
dim(antivirals) # for R/data.R
usethis::use_data(antivirals, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)