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AMR/R/atc.R
dr. M.S. (Matthijs) Berends 53464ff1c8
- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive 
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
2018-03-23 14:46:02 +01:00

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# AUTHORS #
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# LICENCE #
# This program is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License version 2.0, #
# as published by the Free Software Foundation. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# ==================================================================== #
#' Properties of an ATC code
#'
#' 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.}
#' @param atc_code a character or character vector with ATC code(s) of antibiotic(s)
#' @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"}.
#' @param administration type of administration, see \emph{Details}
#' @param url url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.
#' @details
#' Abbreviations for the property \code{"Adm.R"} (parameter \code{administration}):
#' \itemize{
#' \item{\code{"Implant"}}{ = Implant}
#' \item{\code{"Inhal"}}{ = Inhalation}
#' \item{\code{"Instill"}}{ = Instillation}
#' \item{\code{"N"}}{ = nasal}
#' \item{\code{"O"}}{ = oral}
#' \item{\code{"P"}}{ = parenteral}
#' \item{\code{"R"}}{ = rectal}
#' \item{\code{"SL"}}{ = sublingual/buccal}
#' \item{\code{"TD"}}{ = transdermal}
#' \item{\code{"V"}}{ = vaginal}
#' }
#'
#' Abbreviations for the property \code{"U"} (unit):
#' \itemize{
#' \item{\code{"g"}}{ = gram}
#' \item{\code{"mg"}}{ = milligram}
#' \item{\code{"mcg"}}{ = microgram}
#' \item{\code{"U"}}{ = unit}
#' \item{\code{"TU"}}{ = thousand units}
#' \item{\code{"MU"}}{ = million units}
#' \item{\code{"mmol"}}{ = millimole}
#' \item{\code{"ml"}}{ = milliliter (e.g. eyedrops)}
#' }
#' @export
#' @importFrom dplyr %>% progress_estimated
#' @importFrom xml2 read_html
#' @importFrom rvest html_nodes html_table
#' @source \url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
#' @examples
#' \donttest{
#' atc_property("J01CA04", "DDD", "O") # oral DDD (Defined Daily Dose) of amoxicillin
#' atc_property("J01CA04", "DDD", "P") # parenteral DDD (Defined Daily Dose) of amoxicillin
#' }
atc_property <- function(atc_code,
property,
administration = 'O',
url = 'https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no') {
# property <- property %>% tolower()
#
if (property %like% 'unit') {
property <- 'U'
}
# validation of properties
valid_properties.bak <- c("ATC code", "Name", "DDD", "U", "Adm.R", "Note")
valid_properties <- valid_properties.bak #%>% tolower()
if (!property %in% valid_properties) {
stop('Invalid `property`, use one of ', paste(valid_properties, collapse = ", "), '.')
}
returnvalue <- rep(NA_character_, length(atc_code))
if (property == 'DDD') {
returnvalue <- rep(NA_real_, length(atc_code))
}
progress <- progress_estimated(n = length(atc_code))
for (i in 1:length(atc_code)) {
progress$tick()$print()
atc_url <- sub('%s', atc_code[i], url, fixed = TRUE)
tbl <- xml2::read_html(atc_url) %>%
rvest::html_nodes('table') %>%
rvest::html_table(header = TRUE)
if (length(tbl) == 0) {
warning('ATC not found: ', atc_code[i], '. Please check ', atc_url, '.', call. = FALSE)
returnvalue[i] <- NA
next
}
tbl <- tbl[[1]]
if (property == 'Name') {
returnvalue[i] <- tbl[1, 2]
} else {
names(returnvalue)[i] <- tbl[1, 2] %>% as.character()
if (!'Adm.R' %in% colnames(tbl) | is.na(tbl[1, 'Adm.R'])) {
returnvalue[i] <- NA
next
} else {
for (j in 1:nrow(tbl)) {
if (tbl[j, 'Adm.R'] == administration) {
returnvalue[i] <- tbl[j, property]
}
}
}
}
}
cat('\n')
returnvalue
}
#' Name of an antibiotic
#'
#' 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}}.
#' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
#' @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"}.
#' @param textbetween text to put between multiple returned texts
#' @param tolower return output as lower case with function \code{\link{tolower}}.
#' @keywords ab antibiotics
#' @source \code{\link{antibiotics}}
#' @export
#' @importFrom dplyr %>% filter select slice
#' @examples
#' abname("AMCL")
#' # "amoxicillin and enzyme inhibitor"
#'
#' abname("AMCL+GENT")
#' # "amoxicillin and enzyme inhibitor + gentamicin"
#'
#' abname(c("AMCL", "GENT"))
#' # "amoxicillin and enzyme inhibitor" "gentamicin"
#'
#' abname("AMCL", to = "trivial_nl")
#' # "Amoxicilline/clavulaanzuur"
#'
#' abname("AMCL", to = "atc")
#' # "J01CR02"
#'
#' abname("J01CR02", from = "atc", to = "umcg")
#' # "AMCL"
abname <- function(abcode, from = c("guess", "atc", "molis", "umcg"), to = 'official', textbetween = ' + ', tolower = FALSE) {
antibiotics <- AMR::antibiotics
from <- from[1]
if (from == "guess") {
for (i in 1:3) {
if (abcode[1] %in% (antibiotics %>% pull(i))) {
from <- colnames(antibiotics)[i]
}
}
if (from == "guess") {
from <- "umcg"
}
}
colnames(antibiotics) <- colnames(antibiotics) %>% tolower()
from <- from %>% tolower()
to <- to %>% tolower()
if (!from %in% colnames(antibiotics) |
!to %in% colnames(antibiotics)) {
stop(paste0('Invalid `from` or `to`. Choose one of ',
colnames(antibiotics) %>% paste(collapse = ","), '.'), call. = FALSE)
}
abcode <- as.character(abcode)
for (i in 1:length(abcode)) {
drug <- abcode[i]
if (!grepl('+', drug, fixed = TRUE) & !grepl(' en ', drug, fixed = TRUE)) {
# only 1 drug
if (drug %in% (antibiotics %>% pull(from))) {
abcode[i] <-
antibiotics %>%
filter(.[, from] == drug) %>%
select(to) %>%
slice(1) %>%
as.character()
} else {
# not found
warning('Code "', drug, '" not found in antibiotics list.', call. = FALSE)
abcode[i] <- NA
}
} else {
# more than 1 drug
if (grepl('+', drug, fixed = TRUE)) {
drug.group <-
strsplit(drug, '+', fixed = TRUE) %>%
unlist() %>%
trimws('both')
} else if (grepl(' en ', drug, fixed = TRUE)) {
drug.group <-
strsplit(drug, ' en ', fixed = TRUE) %>%
unlist() %>%
trimws('both')
} else {
warning('Invalid concat.')
abcode[i] <- NA
next
}
for (j in 1:length(drug.group)) {
drug.group[j] <-
antibiotics %>%
filter(.[, from] == drug.group[j]) %>%
select(to) %>%
slice(1) %>%
as.character()
if (j > 1 & to %in% c('official', 'trivial_nl')) {
drug.group[j] <- drug.group[j] %>% tolower()
}
}
abcode[i] <- paste(drug.group, collapse = textbetween)
}
}
if (tolower == TRUE) {
abcode <- abcode %>% tolower()
}
abcode
}
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