mirror of
https://github.com/msberends/AMR.git
synced 2025-07-12 18:21:49 +02:00
support veterinary MIC/disk translation
This commit is contained in:
@ -754,12 +754,20 @@ antibiotics <- antibiotics %>%
|
||||
|
||||
# update ATC codes from WHOCC website -------------------------------------
|
||||
|
||||
# last time checked: 2022-10-29
|
||||
# last time checked: 2024-02-22
|
||||
|
||||
library(rvest)
|
||||
updated_atc <- as.list(antibiotics$atc)
|
||||
|
||||
get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
|
||||
get_atcs <- function(ab_name, type = "human") {
|
||||
if (type == "human") {
|
||||
url <- "https://www.whocc.no/atc_ddd_index/"
|
||||
} else if (type == "veterinary") {
|
||||
url <- "https://www.whocc.no/atcvet/atcvet_index/"
|
||||
} else {
|
||||
stop("invalid type")
|
||||
}
|
||||
|
||||
ab_name <- gsub("/", " and ", tolower(ab_name), fixed = TRUE)
|
||||
|
||||
# we will do a search on their website, which means:
|
||||
@ -780,6 +788,7 @@ get_atcs <- function(ab_name, url = "https://www.whocc.no/atc_ddd_index/") {
|
||||
html_node("table") %>%
|
||||
# transform it to an R data set
|
||||
html_table(header = FALSE)
|
||||
|
||||
# and get the ATCs (first column) of only exact hits
|
||||
unique(as.character(atc_tbl[which(tolower(atc_tbl[, 2, drop = TRUE]) == ab_name), 1, drop = TRUE]))
|
||||
}
|
||||
@ -790,7 +799,10 @@ for (i in seq_len(nrow(antibiotics))) {
|
||||
" - Downloading ", antibiotics$name[i],
|
||||
appendLF = FALSE
|
||||
)
|
||||
atcs <- get_atcs(antibiotics$name[i])
|
||||
atcs <- get_atcs(antibiotics$name[i], type = "human")
|
||||
if (all(is.na(atcs))) {
|
||||
atcs <- get_atcs(antibiotics$name[i], type = "veterinary")
|
||||
}
|
||||
if (length(atcs) > 0) {
|
||||
updated_atc[[i]] <- atcs
|
||||
message(" (", length(atcs), " results)")
|
||||
@ -805,7 +817,7 @@ antibiotics$atc <- updated_atc
|
||||
|
||||
# update DDDs from WHOCC website ------------------------------------------
|
||||
|
||||
# last time checked: 2022-10-29
|
||||
# last time checked: 2024-02-22
|
||||
ddd_oral <- rep(NA_real_, nrow(antibiotics))
|
||||
ddd_oral_units <- rep(NA_character_, nrow(antibiotics))
|
||||
ddd_iv <- rep(NA_real_, nrow(antibiotics))
|
||||
|
Reference in New Issue
Block a user