mirror of https://github.com/msberends/AMR.git
240 lines
8.3 KiB
R
240 lines
8.3 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 (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit. \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"}, \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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#' @examples
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#' \donttest{
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#' atc_property("J01CA04", "DDD", "O") # oral DDD (Defined Daily Dose) of amoxicillin
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#' atc_property("J01CA04", "DDD", "P") # parenteral DDD (Defined Daily Dose) of amoxicillin
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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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# 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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#' Name of an antibiotic
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#'
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#' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
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#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
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#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names. WIth \code{from = "guess"} the from will be guessed from \code{"atc"}, \code{"molis"} and \code{"umcg"}.
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#' @param textbetween text to put between multiple returned texts
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#' @param tolower return output as lower case with function \code{\link{tolower}}.
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#' @keywords ab antibiotics
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#' @source \code{\link{antibiotics}}
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#' @export
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#' @importFrom dplyr %>% filter select slice
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#' @examples
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#' abname("AMCL")
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#' # "amoxicillin and enzyme inhibitor"
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#'
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#' abname("AMCL+GENT")
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#' # "amoxicillin and enzyme inhibitor + gentamicin"
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#'
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#' abname(c("AMCL", "GENT"))
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#' # "amoxicillin and enzyme inhibitor" "gentamicin"
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#'
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#' abname("AMCL", to = "trivial_nl")
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#' # "Amoxicilline/clavulaanzuur"
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#'
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#' abname("AMCL", to = "atc")
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#' # "J01CR02"
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#'
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#' abname("J01CR02", from = "atc", to = "umcg")
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#' # "AMCL"
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abname <- function(abcode, from = c("guess", "atc", "molis", "umcg"), to = 'official', textbetween = ' + ', tolower = FALSE) {
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antibiotics <- AMR::antibiotics
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from <- from[1]
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if (from == "guess") {
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for (i in 1:3) {
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if (abcode[1] %in% (antibiotics %>% pull(i))) {
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from <- colnames(antibiotics)[i]
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}
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}
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if (from == "guess") {
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from <- "umcg"
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}
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}
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colnames(antibiotics) <- colnames(antibiotics) %>% tolower()
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from <- from %>% tolower()
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to <- to %>% tolower()
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if (!from %in% colnames(antibiotics) |
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!to %in% colnames(antibiotics)) {
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stop(paste0('Invalid `from` or `to`. Choose one of ',
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colnames(antibiotics) %>% paste(collapse = ","), '.'), call. = FALSE)
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}
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abcode <- as.character(abcode)
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for (i in 1:length(abcode)) {
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drug <- abcode[i]
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if (!grepl('+', drug, fixed = TRUE) & !grepl(' en ', drug, fixed = TRUE)) {
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# only 1 drug
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if (drug %in% (antibiotics %>% pull(from))) {
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abcode[i] <-
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antibiotics %>%
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filter(.[, from] == drug) %>%
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select(to) %>%
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slice(1) %>%
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as.character()
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} else {
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# not found
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warning('Code "', drug, '" not found in antibiotics list.', call. = FALSE)
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abcode[i] <- NA
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}
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} else {
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# more than 1 drug
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if (grepl('+', drug, fixed = TRUE)) {
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drug.group <-
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strsplit(drug, '+', fixed = TRUE) %>%
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unlist() %>%
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trimws('both')
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} else if (grepl(' en ', drug, fixed = TRUE)) {
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drug.group <-
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strsplit(drug, ' en ', fixed = TRUE) %>%
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unlist() %>%
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trimws('both')
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} else {
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warning('Invalid concat.')
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abcode[i] <- NA
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next
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}
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for (j in 1:length(drug.group)) {
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drug.group[j] <-
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antibiotics %>%
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filter(.[, from] == drug.group[j]) %>%
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select(to) %>%
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slice(1) %>%
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as.character()
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if (j > 1 & to %in% c('official', 'trivial_nl')) {
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drug.group[j] <- drug.group[j] %>% tolower()
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}
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}
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abcode[i] <- paste(drug.group, collapse = textbetween)
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}
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}
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if (tolower == TRUE) {
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abcode <- abcode %>% tolower()
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}
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abcode
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}
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