mirror of https://github.com/msberends/AMR.git
122 lines
4.5 KiB
R
122 lines
4.5 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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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 of e.g. an antibiotic.
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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"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"} en \code{"Note"}.
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#' @param administration type of administration, see \emph{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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#' @details
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#' Abbreviations for the property \code{"Adm.R"} (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 for the property \code{"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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#' @importFrom dplyr %>% progress_estimated
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#' @importFrom xml2 read_html
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#' @importFrom rvest html_nodes html_table
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#' @source \url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
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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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# property <- property %>% tolower()
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#
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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.bak <- c("ATC code", "Name", "DDD", "U", "Adm.R", "Note")
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valid_properties <- valid_properties.bak #%>% tolower()
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if (!property %in% valid_properties) {
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stop('Invalid `property`, use one of ', paste(valid_properties, collapse = ", "), '.')
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}
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returnvalue <- rep(NA_character_, length(atc_code))
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if (property == 'DDD') {
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returnvalue <- rep(NA_real_, 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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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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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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tbl <- tbl[[1]]
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if (property == 'Name') {
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returnvalue[i] <- tbl[1, 2]
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} else {
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names(returnvalue)[i] <- tbl[1, 2] %>% as.character()
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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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cat('\n')
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returnvalue
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}
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