mirror of https://github.com/msberends/AMR.git
207 lines
8.1 KiB
R
207 lines
8.1 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data Analysis for R #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2021 Berends MS, Luz CF et al. #
|
|
# Developed at the University of Groningen, the Netherlands, in #
|
|
# collaboration with non-profit organisations Certe Medical #
|
|
# Diagnostics & Advice, and University Medical Center Groningen. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# #
|
|
# Visit our website for the full manual and a complete tutorial about #
|
|
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
|
# ==================================================================== #
|
|
|
|
#' Get ATC Properties from WHOCC Website
|
|
#'
|
|
#' 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.
|
|
#' @inheritSection lifecycle Stable Lifecycle
|
|
#' @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 `"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*.
|
|
#' @param administration type of administration when using `property = "Adm.R"`, see *Details*
|
|
#' @param url url of website of the WHOCC. The sign `%s` can be used as a placeholder for ATC codes.
|
|
#' @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").
|
|
#' @param ... arguments to pass on to `atc_property`
|
|
#' @details
|
|
#' Options for argument `administration`:
|
|
#'
|
|
#' - `"Implant"` = Implant
|
|
#' - `"Inhal"` = Inhalation
|
|
#' - `"Instill"` = Instillation
|
|
#' - `"N"` = nasal
|
|
#' - `"O"` = oral
|
|
#' - `"P"` = parenteral
|
|
#' - `"R"` = rectal
|
|
#' - `"SL"` = sublingual/buccal
|
|
#' - `"TD"` = transdermal
|
|
#' - `"V"` = vaginal
|
|
#'
|
|
#' Abbreviations of return values when using `property = "U"` (unit):
|
|
#'
|
|
#' - `"g"` = gram
|
|
#' - `"mg"` = milligram
|
|
#' - `"mcg"`` = microgram
|
|
#' - `"U"` = unit
|
|
#' - `"TU"` = thousand units
|
|
#' - `"MU"` = million units
|
|
#' - `"mmol"` = millimole
|
|
#' - `"ml"` = milliliter (e.g. eyedrops)
|
|
#'
|
|
#' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
|
|
#' @export
|
|
#' @rdname atc_online
|
|
#' @inheritSection AMR Read more on Our Website!
|
|
#' @source <https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/>
|
|
#' @examples
|
|
#' \donttest{
|
|
#' # oral DDD (Defined Daily Dose) of amoxicillin
|
|
#' atc_online_property("J01CA04", "DDD", "O")
|
|
#'
|
|
#' # parenteral DDD (Defined Daily Dose) of amoxicillin
|
|
#' atc_online_property("J01CA04", "DDD", "P")
|
|
#'
|
|
#' atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
|
#' }
|
|
atc_online_property <- function(atc_code,
|
|
property,
|
|
administration = "O",
|
|
url = "https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no",
|
|
url_vet = "https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no") {
|
|
meet_criteria(atc_code, allow_class = "character")
|
|
meet_criteria(property, allow_class = "character", has_length = 1, is_in = c("ATC", "Name", "DDD", "U", "Adm.R", "Note", "groups"), ignore.case = TRUE)
|
|
meet_criteria(administration, allow_class = "character", has_length = 1)
|
|
meet_criteria(url, allow_class = "character", has_length = 1, looks_like = "https?://")
|
|
meet_criteria(url_vet, allow_class = "character", has_length = 1, looks_like = "https?://")
|
|
|
|
has_internet <- import_fn("has_internet", "curl")
|
|
html_attr <- import_fn("html_attr", "rvest")
|
|
html_children <- import_fn("html_children", "rvest")
|
|
html_node <- import_fn("html_node", "rvest")
|
|
html_nodes <- import_fn("html_nodes", "rvest")
|
|
html_table <- import_fn("html_table", "rvest")
|
|
html_text <- import_fn("html_text", "rvest")
|
|
read_html <- import_fn("read_html", "xml2")
|
|
|
|
check_dataset_integrity()
|
|
|
|
if (!all(atc_code %in% antibiotics)) {
|
|
atc_code <- as.character(ab_atc(atc_code))
|
|
}
|
|
|
|
if (!has_internet()) {
|
|
message_("There appears to be no internet connection, returning NA.",
|
|
add_fn = font_red,
|
|
as_note = FALSE)
|
|
return(rep(NA, length(atc_code)))
|
|
}
|
|
|
|
# also allow unit as property
|
|
if (property %like% "unit") {
|
|
property <- "U"
|
|
}
|
|
|
|
property <- tolower(property)
|
|
if (property == "ddd") {
|
|
returnvalue <- rep(NA_real_, length(atc_code))
|
|
} else if (property == "groups") {
|
|
returnvalue <- list()
|
|
} else {
|
|
returnvalue <- rep(NA_character_, length(atc_code))
|
|
}
|
|
|
|
progress <- progress_ticker(n = length(atc_code), 3)
|
|
on.exit(close(progress))
|
|
|
|
for (i in seq_len(length(atc_code))) {
|
|
|
|
progress$tick()
|
|
|
|
if (atc_code[i] %like% "^Q") {
|
|
# veterinary drugs, ATC_vet codes start with a "Q"
|
|
atc_url <- url_vet
|
|
} else {
|
|
atc_url <- url
|
|
}
|
|
atc_url <- sub("%s", atc_code[i], atc_url, fixed = TRUE)
|
|
|
|
if (property == "groups") {
|
|
tbl <- read_html(atc_url) %pm>%
|
|
html_node("#content") %pm>%
|
|
html_children() %pm>%
|
|
html_node("a")
|
|
|
|
# get URLS of items
|
|
hrefs <- tbl %pm>% html_attr("href")
|
|
# get text of items
|
|
texts <- tbl %pm>% html_text()
|
|
# select only text items where URL like "code="
|
|
texts <- texts[grepl("?code=", tolower(hrefs), fixed = TRUE)]
|
|
# last one is antibiotics, skip it
|
|
texts <- texts[seq_len(length(texts)) - 1]
|
|
returnvalue <- c(list(texts), returnvalue)
|
|
|
|
} else {
|
|
tbl <- read_html(atc_url) %pm>%
|
|
html_nodes("table") %pm>%
|
|
html_table(header = TRUE) %pm>%
|
|
as.data.frame(stringsAsFactors = FALSE)
|
|
|
|
# case insensitive column names
|
|
colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
|
|
|
|
if (length(tbl) == 0) {
|
|
warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
|
|
returnvalue[i] <- NA
|
|
next
|
|
}
|
|
|
|
if (property %in% c("atc", "name")) {
|
|
# ATC and name are only in first row
|
|
returnvalue[i] <- tbl[1, property]
|
|
} else {
|
|
if (!"adm.r" %in% colnames(tbl) | is.na(tbl[1, "adm.r"])) {
|
|
returnvalue[i] <- NA
|
|
next
|
|
} else {
|
|
for (j in seq_len(nrow(tbl))) {
|
|
if (tbl[j, "adm.r"] == administration) {
|
|
returnvalue[i] <- tbl[j, property]
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
if (property == "groups" & length(returnvalue) == 1) {
|
|
returnvalue <- returnvalue[[1]]
|
|
}
|
|
|
|
returnvalue
|
|
}
|
|
|
|
#' @rdname atc_online
|
|
#' @export
|
|
atc_online_groups <- function(atc_code, ...) {
|
|
meet_criteria(atc_code, allow_class = "character")
|
|
atc_online_property(atc_code = atc_code, property = "groups", ...)
|
|
}
|
|
|
|
#' @rdname atc_online
|
|
#' @export
|
|
atc_online_ddd <- function(atc_code, ...) {
|
|
meet_criteria(atc_code, allow_class = "character")
|
|
atc_online_property(atc_code = atc_code, property = "ddd", ...)
|
|
}
|