AMR/R/ab_class_selectors.R

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R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) 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 analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Antibiotic class selectors
#'
#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' @inheritParams filter_ab_class
#' @details These functions only work in R 3.2 (2015) and later.
#'
#' All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#' @rdname antibiotic_class_selectors
#' @seealso [filter_ab_class()] for the `filter()` equivalent.
#' @name antibiotic_class_selectors
#' @export
#' @inheritSection AMR Reference data publicly available
#' @inheritSection AMR Read more on our website!
#' @examples
#' # `example_isolates` is a dataset available in the AMR package.
#' # See ?example_isolates.
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates[, c(carbapenems())]
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
#' example_isolates[, c("mo", aminoglycosides())]
#'
#' if (require("dplyr")) {
#'
#' # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
#' example_isolates %>%
#' select(carbapenems())
#'
#' # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
#' example_isolates %>%
#' select(mo, aminoglycosides())
#'
#' # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
#' example_isolates %>%
#' select(mo, ab_class("mycobact"))
#'
#'
#' # get bug/drug combinations for only macrolides in Gram-positives:
#' example_isolates %>%
#' filter(mo_is_gram_positive()) %>%
#' select(mo, macrolides()) %>%
#' bug_drug_combinations() %>%
#' format()
#'
#'
#' data.frame(some_column = "some_value",
#' J01CA01 = "S") %>% # ATC code of ampicillin
#' select(penicillins()) # only the 'J01CA01' column will be selected
#'
#'
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
#' # (though the row names on the first are more correct)
#' example_isolates %>% filter_carbapenems("R", "all")
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
#' }
ab_class <- function(ab_class) {
ab_selector(ab_class, function_name = "ab_class")
}
#' @rdname antibiotic_class_selectors
#' @export
aminoglycosides <- function() {
ab_selector("aminoglycoside", function_name = "aminoglycosides")
}
#' @rdname antibiotic_class_selectors
#' @export
carbapenems <- function() {
ab_selector("carbapenem", function_name = "carbapenems")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins <- function() {
ab_selector("cephalosporin", function_name = "cephalosporins")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_1st <- function() {
ab_selector("cephalosporins.*1", function_name = "cephalosporins_1st")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_2nd <- function() {
ab_selector("cephalosporins.*2", function_name = "cephalosporins_2nd")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_3rd <- function() {
ab_selector("cephalosporins.*3", function_name = "cephalosporins_3rd")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_4th <- function() {
ab_selector("cephalosporins.*4", function_name = "cephalosporins_4th")
}
#' @rdname antibiotic_class_selectors
#' @export
cephalosporins_5th <- function() {
ab_selector("cephalosporins.*5", function_name = "cephalosporins_5th")
}
#' @rdname antibiotic_class_selectors
#' @export
fluoroquinolones <- function() {
ab_selector("fluoroquinolone", function_name = "fluoroquinolones")
}
#' @rdname antibiotic_class_selectors
#' @export
glycopeptides <- function() {
ab_selector("glycopeptide", function_name = "glycopeptides")
}
#' @rdname antibiotic_class_selectors
#' @export
macrolides <- function() {
ab_selector("macrolide", function_name = "macrolides")
}
#' @rdname antibiotic_class_selectors
#' @export
penicillins <- function() {
ab_selector("penicillin", function_name = "penicillins")
}
#' @rdname antibiotic_class_selectors
#' @export
tetracyclines <- function() {
ab_selector("tetracycline", function_name = "tetracyclines")
}
ab_selector <- function(ab_class, function_name) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
return(NULL)
}
vars_df <- get_current_data(arg_name = NA, call = -3)
ab_in_data <- get_column_abx(vars_df, info = FALSE)
if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found.")
return(NULL)
}
ab_reference <- subset(antibiotics,
group %like% ab_class |
atc_group1 %like% ab_class |
atc_group2 %like% ab_class)
ab_group <- find_ab_group(ab_class)
if (ab_group == "") {
ab_group <- paste0("'", ab_class, "'")
examples <- ""
} else {
examples <- paste0(" (such as ", find_ab_names(ab_class, 2), ")")
}
# get the columns with a group names in the chosen ab class
agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
if (message_not_thrown_before(function_name)) {
if (length(agents) == 0) {
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
} else {
message_("Selecting ", ab_group, ": ",
paste(paste0("column '", font_bold(agents, collapse = NULL),
"' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
collapse = ", "),
as_note = FALSE,
extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
}
remember_thrown_message(function_name)
}
unname(agents)
}