mirror of https://github.com/msberends/AMR.git
205 lines
8.0 KiB
R
205 lines
8.0 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Get ATC properties from WHOCC website
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#'
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#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic), such as the name, defined daily dose (DDD) or standard unit.
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#' @inheritSection lifecycle Stable lifecycle
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#' @param atc_code a character or character vector with ATC code(s) of antibiotic(s)
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#' @param property property of an ATC code. Valid values are `"ATC"`, `"Name"`, `"DDD"`, `"U"` (`"unit"`), `"Adm.R"`, `"Note"` and `groups`. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.
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#' @param administration type of administration when using `property = "Adm.R"`, see Details
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#' @param url url of website of the WHOCC. The sign `%s` can be used as a placeholder for ATC codes.
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#' @param url_vet url of website of the WHOCC for veterinary medicine. The sign `%s` can be used as a placeholder for ATC_vet codes (that all start with "Q").
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#' @param ... parameters to pass on to `atc_property`
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#' @details
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#' Options for parameter `administration`:
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#'
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#' - `"Implant"` = Implant
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#' - `"Inhal"` = Inhalation
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#' - `"Instill"` = Instillation
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#' - `"N"` = nasal
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#' - `"O"` = oral
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#' - `"P"` = parenteral
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#' - `"R"` = rectal
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#' - `"SL"` = sublingual/buccal
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#' - `"TD"` = transdermal
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#' - `"V"` = vaginal
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#'
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#' Abbreviations of return values when using `property = "U"` (unit):
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#'
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#' - `"g"` = gram
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#' - `"mg"` = milligram
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#' - `"mcg"`` = microgram
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#' - `"U"` = unit
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#' - `"TU"` = thousand units
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#' - `"MU"` = million units
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#' - `"mmol"` = millimole
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#' - `"ml"` = milliliter (e.g. eyedrops)
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#'
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#' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
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#' @export
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#' @rdname atc_online
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#' @inheritSection AMR Read more on our website!
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#' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
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#' @examples
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#' \donttest{
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#' # oral DDD (Defined Daily Dose) of amoxicillin
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#' atc_online_property("J01CA04", "DDD", "O")
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#'
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#' # parenteral DDD (Defined Daily Dose) of amoxicillin
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#' atc_online_property("J01CA04", "DDD", "P")
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#'
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#' atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
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#' }
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atc_online_property <- function(atc_code,
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property,
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administration = "O",
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url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
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url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
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meet_criteria(atc_code, allow_class = "character")
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meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups"), ignore.case = TRUE)
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meet_criteria(administration, allow_class = "character", has_length = 1)
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meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
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meet_criteria(url_vet, allow_class = "character", has_length = 1, looks_like = "https?://")
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has_internet <- import_fn("has_internet", "curl")
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html_attr <- import_fn("html_attr", "rvest")
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html_children <- import_fn("html_children", "rvest")
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html_node <- import_fn("html_node", "rvest")
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html_nodes <- import_fn("html_nodes", "rvest")
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html_table <- import_fn("html_table", "rvest")
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html_text <- import_fn("html_text", "rvest")
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read_html <- import_fn("read_html", "xml2")
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check_dataset_integrity()
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if (!all(atc_code %in% antibiotics)) {
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atc_code <- as.character(ab_atc(atc_code))
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}
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if (!has_internet()) {
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message("There appears to be no internet connection, returning NA.")
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return(rep(NA, length(atc_code)))
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}
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# also allow unit as property
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if (property %like% "unit") {
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property <- "U"
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}
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property <- tolower(property)
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if (property == "ddd") {
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returnvalue <- rep(NA_real_, length(atc_code))
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} else if (property == "groups") {
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returnvalue <- list()
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} else {
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returnvalue <- rep(NA_character_, length(atc_code))
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}
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progress <- progress_ticker(n = length(atc_code), 3)
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on.exit(close(progress))
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for (i in seq_len(length(atc_code))) {
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progress$tick()
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if (atc_code[i] %like% "^Q") {
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# veterinary drugs, ATC_vet codes start with a "Q"
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atc_url <- url_vet
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} else {
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atc_url <- url
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}
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atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE)
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if (property == "groups") {
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tbl <- read_html(atc_url) %pm>%
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html_node("#content") %pm>%
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html_children() %pm>%
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html_node("a")
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# get URLS of items
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hrefs <- tbl %pm>% html_attr("href")
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# get text of items
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texts <- tbl %pm>% html_text()
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# select only text items where URL like "code="
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texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
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# last one is antibiotics, skip it
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texts <- texts[seq_len(length(texts)) - 1]
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returnvalue <- c(list(texts), returnvalue)
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} else {
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tbl <- read_html(atc_url) %pm>%
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html_nodes("table") %pm>%
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html_table(header = TRUE) %pm>%
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as.data.frame(stringsAsFactors = FALSE)
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# case insensitive column names
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colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
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if (length(tbl) == 0) {
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warning("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call. = FALSE)
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returnvalue[i] <- NA
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next
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}
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if (property %in% c("atc", "name")) {
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# ATC and name are only in first row
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returnvalue[i] <- tbl[1, property]
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} else {
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if (!"adm.r" %in% colnames(tbl) | is.na(tbl[1, "adm.r"])) {
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returnvalue[i] <- NA
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next
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} else {
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for (j in seq_len(nrow(tbl))) {
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if (tbl[j, "adm.r"] == administration) {
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returnvalue[i] <- tbl[j, property]
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}
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}
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}
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}
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}
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}
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if (property == "groups" & length(returnvalue) == 1) {
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returnvalue <- returnvalue[[1]]
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}
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returnvalue
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}
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#' @rdname atc_online
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#' @export
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atc_online_groups <- function(atc_code, ...) {
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meet_criteria(atc_code, allow_class = "character")
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atc_online_property(atc_code = atc_code, property = "groups", ...)
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}
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#' @rdname atc_online
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#' @export
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atc_online_ddd <- function(atc_code, ...) {
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meet_criteria(atc_code, allow_class = "character")
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atc_online_property(atc_code = atc_code, property = "ddd", ...)
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}
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