mirror of https://github.com/msberends/AMR.git
129 lines
5.0 KiB
R
129 lines
5.0 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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#' Create identifier of an isolate
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#'
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#' This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.
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#' @inheritSection lifecycle Maturing lifecycle
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#' @inheritParams eucast_rules
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#' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglysides()]
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # automatic selection of microorganism and antibiotics (i.e., all <rsi> columns, see ?as.rsi)
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#' x <- isolate_identifier(example_isolates)
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#'
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#' # ignore microorganism codes, only use antimicrobial results
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#' x <- isolate_identifier(example_isolates, col_mo = FALSE, cols_ab = c("AMX", "TZP", "GEN", "TOB"))
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#'
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#' # select antibiotics from certain antibiotic classes
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#' x <- isolate_identifier(example_isolates, cols_ab = c(carbapenems(), aminoglycosides()))
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isolate_identifier <- function(x, col_mo = NULL, cols_ab = NULL) {
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(x, "mo")
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}
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if (isFALSE(col_mo)) {
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# is FALSE then ignore mo column
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x$col_mo <- ""
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col_mo <- "col_mo"
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} else if (!is.null(col_mo)) {
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x[, col_mo] <- paste0(as.mo(x[, col_mo, drop = TRUE]), "|")
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}
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cols_ab <- deparse(substitute(cols_ab)) # support ab class selectors: isolate_identifier(x, cols_ab = carbapenems())
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if (identical(cols_ab, "NULL")) {
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cols_ab <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.rsi)]
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} else {
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cols_ab <- tryCatch(colnames(x[, eval(parse(text = cols_ab), envir = parent.frame())]),
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# tryCatch adds 4 calls, so total is -5
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error = function(e) stop_(e$message, call = -5))
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}
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if (length(cols_ab) == 0) {
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warning_("no columns with antimicrobial agents found", call = TRUE)
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}
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out <- x[, c(col_mo, cols_ab), drop = FALSE]
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out <- do.call(paste, c(out, sep = ""))
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out <- gsub("NA", ".", out, fixed = TRUE)
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set_clean_class(out, new_class = c("isolate_identifier", "character"))
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}
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#' @method print isolate_identifier
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#' @export
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#' @noRd
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print.isolate_identifier <- function(x, ...) {
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print(as.character(x), ...)
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}
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#' @method [ isolate_identifier
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#' @export
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#' @noRd
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"[.isolate_identifier" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method [[ isolate_identifier
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#' @export
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#' @noRd
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"[[.isolate_identifier" <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method [<- isolate_identifier
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#' @export
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#' @noRd
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"[<-.isolate_identifier" <- function(i, j, ..., value) {
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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}
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#' @method [[<- isolate_identifier
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#' @export
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#' @noRd
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"[[<-.isolate_identifier" <- function(i, j, ..., value) {
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y <- NextMethod()
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attributes(y) <- attributes(i)
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y
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}
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#' @method c isolate_identifier
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#' @export
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#' @noRd
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c.isolate_identifier <- function(x, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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#' @method unique isolate_identifier
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#' @export
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#' @noRd
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unique.isolate_identifier <- function(x, incomparables = FALSE, ...) {
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y <- NextMethod()
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attributes(y) <- attributes(x)
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y
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}
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