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atc_ functions
This commit is contained in:
188
R/atc.R
188
R/atc.R
@ -186,191 +186,3 @@ as.data.frame.atc <- function (x, ...) {
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pull.atc <- function(.data, ...) {
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pull(as.data.frame(.data), ...)
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}
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#' Properties of an ATC code
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#'
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#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \cr \strong{This function requires an internet connection.}
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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 \code{"ATC"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"}, \code{"Note"} and \code{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 \code{property = "Adm.R"}, see Details
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#' @param url url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.
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#' @param ... parameters to pass on to \code{atc_property}
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#' @details
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#' Options for parameter \code{administration}:
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#' \itemize{
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#' \item{\code{"Implant"}}{ = Implant}
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#' \item{\code{"Inhal"}}{ = Inhalation}
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#' \item{\code{"Instill"}}{ = Instillation}
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#' \item{\code{"N"}}{ = nasal}
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#' \item{\code{"O"}}{ = oral}
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#' \item{\code{"P"}}{ = parenteral}
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#' \item{\code{"R"}}{ = rectal}
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#' \item{\code{"SL"}}{ = sublingual/buccal}
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#' \item{\code{"TD"}}{ = transdermal}
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#' \item{\code{"V"}}{ = vaginal}
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#' }
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#'
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#' Abbreviations of return values when using \code{property = "U"} (unit):
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#' \itemize{
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#' \item{\code{"g"}}{ = gram}
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#' \item{\code{"mg"}}{ = milligram}
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#' \item{\code{"mcg"}}{ = microgram}
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#' \item{\code{"U"}}{ = unit}
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#' \item{\code{"TU"}}{ = thousand units}
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#' \item{\code{"MU"}}{ = million units}
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#' \item{\code{"mmol"}}{ = millimole}
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#' \item{\code{"ml"}}{ = milliliter (e.g. eyedrops)}
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#' }
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#' @export
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#' @rdname atc_property
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#' @importFrom dplyr %>% progress_estimated
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#' @importFrom xml2 read_html
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#' @importFrom rvest html_children html_node html_nodes html_table
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#' @importFrom curl nslookup
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#' @source \url{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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#' # What's the ATC of amoxicillin?
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#' guess_atc("Amoxicillin")
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#' # [1] "J01CA04"
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#'
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#' # oral DDD (Defined Daily Dose) of amoxicillin
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#' atc_property("J01CA04", "DDD", "O")
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#' # parenteral DDD (Defined Daily Dose) of amoxicillin
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#' atc_property("J01CA04", "DDD", "P")
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#'
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#' atc_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
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#' # [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
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#' # [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
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#' # [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
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#' # [4] "Penicillins with extended spectrum"
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#' }
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atc_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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# check active network interface, from https://stackoverflow.com/a/5078002/4575331
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has_internet <- function(url) {
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# extract host from given url
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# https://www.whocc.no/atc_ddd_index/ -> www.whocc.no
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url <- url %>%
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gsub("^(http://|https://)", "", .) %>%
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strsplit('/', fixed = TRUE) %>%
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unlist() %>%
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.[1]
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!is.null(curl::nslookup(url, error = FALSE))
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}
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# check for connection using the ATC of amoxicillin
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if (!has_internet(url = url)) {
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message("The URL could not be reached.")
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return(rep(NA, length(atc_code)))
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}
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if (length(property) != 1L) {
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stop('`property` must be of length 1', call. = FALSE)
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}
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if (length(administration) != 1L) {
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stop('`administration` must be of length 1', call. = FALSE)
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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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# validation of properties
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valid_properties <- c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups")
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valid_properties.bak <- valid_properties
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property <- tolower(property)
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valid_properties <- tolower(valid_properties)
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if (!property %in% valid_properties) {
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stop('Invalid `property`, use one of ', paste(valid_properties.bak, collapse = ", "), '.')
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}
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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_estimated(n = length(atc_code))
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for (i in 1:length(atc_code)) {
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progress$tick()$print()
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atc_url <- sub('%s', atc_code[i], url, fixed = TRUE)
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if (property == "groups") {
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tbl <- xml2::read_html(atc_url) %>%
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rvest::html_node("#content") %>%
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rvest::html_children() %>%
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rvest::html_node("a")
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# get URLS of items
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hrefs <- tbl %>% rvest::html_attr("href")
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# get text of items
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texts <- tbl %>% rvest::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[1:length(texts) - 1]
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returnvalue <- c(list(texts), returnvalue)
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} else {
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tbl <- xml2::read_html(atc_url) %>%
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rvest::html_nodes('table') %>%
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rvest::html_table(header = TRUE) %>%
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as.data.frame(stringsAsFactors = FALSE)
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# case insensitive column names
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colnames(tbl) <- tolower(colnames(tbl)) %>% gsub('^atc.*', 'atc', .)
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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 1: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_property
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#' @export
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atc_groups <- function(atc_code, ...) {
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atc_property(atc_code = atc_code, property = "groups", ...)
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}
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#' @rdname atc_property
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#' @export
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atc_ddd <- function(atc_code, ...) {
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atc_property(atc_code = atc_code, property = "ddd", ...)
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}
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204
R/atc_online.R
Normal file
204
R/atc_online.R
Normal file
@ -0,0 +1,204 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' Properties of an ATC code
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#'
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#' Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \cr \strong{This function requires an internet connection.}
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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 \code{"ATC"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"}, \code{"Note"} and \code{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 \code{property = "Adm.R"}, see Details
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#' @param url url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.
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#' @param ... parameters to pass on to \code{atc_property}
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#' @details
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#' Options for parameter \code{administration}:
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#' \itemize{
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#' \item{\code{"Implant"}}{ = Implant}
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#' \item{\code{"Inhal"}}{ = Inhalation}
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#' \item{\code{"Instill"}}{ = Instillation}
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#' \item{\code{"N"}}{ = nasal}
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#' \item{\code{"O"}}{ = oral}
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#' \item{\code{"P"}}{ = parenteral}
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#' \item{\code{"R"}}{ = rectal}
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#' \item{\code{"SL"}}{ = sublingual/buccal}
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#' \item{\code{"TD"}}{ = transdermal}
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#' \item{\code{"V"}}{ = vaginal}
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#' }
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#'
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#' Abbreviations of return values when using \code{property = "U"} (unit):
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#' \itemize{
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#' \item{\code{"g"}}{ = gram}
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#' \item{\code{"mg"}}{ = milligram}
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#' \item{\code{"mcg"}}{ = microgram}
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#' \item{\code{"U"}}{ = unit}
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#' \item{\code{"TU"}}{ = thousand units}
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#' \item{\code{"MU"}}{ = million units}
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#' \item{\code{"mmol"}}{ = millimole}
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#' \item{\code{"ml"}}{ = milliliter (e.g. eyedrops)}
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#' }
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#' @export
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#' @rdname atc_online
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#' @importFrom dplyr %>% progress_estimated
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#' @importFrom xml2 read_html
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#' @importFrom rvest html_children html_node html_nodes html_table
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#' @importFrom curl nslookup
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#' @source \url{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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#' # 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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#' # [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
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#' # [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
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#' # [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
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#' # [4] "Penicillins with extended spectrum"
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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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# check active network interface, from https://stackoverflow.com/a/5078002/4575331
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has_internet <- function(url) {
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# extract host from given url
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# https://www.whocc.no/atc_ddd_index/ -> www.whocc.no
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url <- url %>%
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gsub("^(http://|https://)", "", .) %>%
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strsplit('/', fixed = TRUE) %>%
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unlist() %>%
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.[1]
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!is.null(curl::nslookup(url, error = FALSE))
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}
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# check for connection using the ATC of amoxicillin
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if (!has_internet(url = url)) {
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message("The URL could not be reached.")
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return(rep(NA, length(atc_code)))
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}
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if (length(property) != 1L) {
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stop('`property` must be of length 1', call. = FALSE)
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}
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if (length(administration) != 1L) {
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stop('`administration` must be of length 1', call. = FALSE)
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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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# validation of properties
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valid_properties <- c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups")
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valid_properties.bak <- valid_properties
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property <- tolower(property)
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valid_properties <- tolower(valid_properties)
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if (!property %in% valid_properties) {
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stop('Invalid `property`, use one of ', paste(valid_properties.bak, collapse = ", "), '.')
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}
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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_estimated(n = length(atc_code))
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for (i in 1:length(atc_code)) {
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progress$tick()$print()
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atc_url <- sub('%s', atc_code[i], url, fixed = TRUE)
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if (property == "groups") {
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tbl <- xml2::read_html(atc_url) %>%
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rvest::html_node("#content") %>%
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rvest::html_children() %>%
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rvest::html_node("a")
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# get URLS of items
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hrefs <- tbl %>% rvest::html_attr("href")
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# get text of items
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texts <- tbl %>% rvest::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[1:length(texts) - 1]
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returnvalue <- c(list(texts), returnvalue)
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} else {
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tbl <- xml2::read_html(atc_url) %>%
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rvest::html_nodes('table') %>%
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rvest::html_table(header = TRUE) %>%
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as.data.frame(stringsAsFactors = FALSE)
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# case insensitive column names
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colnames(tbl) <- tolower(colnames(tbl)) %>% gsub('^atc.*', 'atc', .)
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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 1: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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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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atc_online_property(atc_code = atc_code, property = "ddd", ...)
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}
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@ -25,20 +25,20 @@
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#' @param x a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}
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#' @param property one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}
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#' @param language language of the returned text, defaults to English (\code{"en"}) and can be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).
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#' @rdname ab_property
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#' @return A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
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#' @rdname atc_property
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#' @return A vector of values. In case of \code{atc_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
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#' @export
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||||
#' @importFrom dplyr %>% left_join pull
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#' @seealso \code{\link{antibiotics}}
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#' @inheritSection AMR Read more on our website!
|
||||
#' @examples
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||||
#' ab_atc("amcl") # J01CR02
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#' ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
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#' ab_name("amcl", "nl") # Amoxicilline met enzymremmer
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#' ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
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#' ab_certe("amcl") # amcl
|
||||
#' ab_umcg("amcl") # AMCL
|
||||
ab_property <- function(x, property = 'official') {
|
||||
#' as.atc("amcl") # J01CR02
|
||||
#' atc_name("amcl") # Amoxicillin and beta-lactamase inhibitor
|
||||
#' atc_name("amcl", "nl") # Amoxicilline met enzymremmer
|
||||
#' atc_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
|
||||
#' atc_certe("amcl") # amcl
|
||||
#' atc_umcg("amcl") # AMCL
|
||||
atc_property <- function(x, property = 'official') {
|
||||
property <- property[1]
|
||||
if (!property %in% colnames(AMR::antibiotics)) {
|
||||
stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
|
||||
@ -53,15 +53,9 @@ ab_property <- function(x, property = 'official') {
|
||||
)
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_atc <- function(x) {
|
||||
as.character(as.atc(x))
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @export
|
||||
ab_official <- function(x, language = NULL) {
|
||||
atc_official <- function(x, language = NULL) {
|
||||
|
||||
if (is.null(language)) {
|
||||
language <- getOption("AMR_locale", default = "en")[1L]
|
||||
@ -69,40 +63,40 @@ ab_official <- function(x, language = NULL) {
|
||||
language <- tolower(language[1])
|
||||
}
|
||||
if (language %in% c("en", "")) {
|
||||
ab_property(x, "official")
|
||||
atc_property(x, "official")
|
||||
} else if (language == "nl") {
|
||||
ab_property(x, "official_nl")
|
||||
atc_property(x, "official_nl")
|
||||
} else {
|
||||
stop("Unsupported language: '", language, "' - use one of: 'en', 'nl'", call. = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_name <- ab_official
|
||||
atc_name <- atc_official
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_trivial_nl <- function(x) {
|
||||
ab_property(x, "trivial_nl")
|
||||
atc_trivial_nl <- function(x) {
|
||||
atc_property(x, "trivial_nl")
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_certe <- function(x) {
|
||||
ab_property(x, "certe")
|
||||
atc_certe <- function(x) {
|
||||
atc_property(x, "certe")
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_umcg <- function(x) {
|
||||
ab_property(x, "umcg")
|
||||
atc_umcg <- function(x) {
|
||||
atc_property(x, "umcg")
|
||||
}
|
||||
|
||||
#' @rdname ab_property
|
||||
#' @rdname atc_property
|
||||
#' @export
|
||||
ab_tradenames <- function(x) {
|
||||
res <- ab_property(x, "trade_name")
|
||||
atc_tradenames <- function(x) {
|
||||
res <- atc_property(x, "trade_name")
|
||||
res <- strsplit(res, "|", fixed = TRUE)
|
||||
if (length(x) == 1) {
|
||||
res <- unlist(res)
|
||||
@ -21,7 +21,7 @@
|
||||
|
||||
#' Deprecated functions
|
||||
#'
|
||||
#' These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.
|
||||
#' These functions are so-called '\link{Deprecated}'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
#' @export
|
||||
#' @keywords internal
|
||||
@ -53,3 +53,59 @@ guess_mo <- function(...) {
|
||||
.Deprecated(new = "as.mo", package = "AMR")
|
||||
as.mo(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_property <- function(...) {
|
||||
.Deprecated(new = "atc_property", package = "AMR")
|
||||
atc_property(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_atc <- function(...) {
|
||||
.Deprecated(new = "as.atc", package = "AMR")
|
||||
as.atc(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_official <- function(...) {
|
||||
.Deprecated(new = "atc_official", package = "AMR")
|
||||
atc_official(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_name <- function(...) {
|
||||
.Deprecated(new = "atc_name", package = "AMR")
|
||||
atc_name(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_trivial_nl <- function(...) {
|
||||
.Deprecated(new = "atc_trivial_nl", package = "AMR")
|
||||
atc_trivial_nl(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_certe <- function(...) {
|
||||
.Deprecated(new = "atc_certe", package = "AMR")
|
||||
atc_certe(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_umcg <- function(...) {
|
||||
.Deprecated(new = "atc_umcg", package = "AMR")
|
||||
atc_umcg(...)
|
||||
}
|
||||
|
||||
#' @rdname AMR-deprecated
|
||||
#' @export
|
||||
ab_tradenames <- function(...) {
|
||||
.Deprecated(new = "atc_tradenames", package = "AMR")
|
||||
atc_tradenames(...)
|
||||
}
|
||||
|
||||
2
R/zzz.R
2
R/zzz.R
@ -25,7 +25,7 @@
|
||||
#' @details
|
||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
|
||||
#'
|
||||
#' This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
#' This package was created for both academic research and routine analysis by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
#' @section Read more on our website!:
|
||||
#' \if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
#' On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
|
||||
|
||||
Reference in New Issue
Block a user