mirror of https://github.com/msberends/AMR.git
149 lines
4.5 KiB
R
149 lines
4.5 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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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) 2018-2020 Berends MS, Luz CF et al. #
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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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# #
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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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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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#' Class 'disk'
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#'
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#' This transforms a vector to a new class [`disk`], which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
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#' @inheritSection lifecycle Stable lifecycle
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#' @rdname as.disk
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#' @param x vector
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#' @param na.rm a logical indicating whether missing values should be removed
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#' @details Interpret disk values as RSI values with [as.rsi()]. It supports guidelines from EUCAST and CLSI.
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#' @return An [`integer`] with additional new class [`disk`]
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#' @aliases disk
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#' @export
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#' @seealso [as.rsi()]
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' \dontrun{
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#' # transform existing disk zones to the `disk` class
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#' library(dplyr)
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#' df <- data.frame(microorganism = "E. coli",
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#' AMP = 20,
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#' CIP = 14,
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#' GEN = 18,
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#' TOB = 16)
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#' df <- df %>% mutate_at(vars(AMP:TOB), as.disk)
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#' df
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#'
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#' # interpret disk values, see ?as.rsi
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#' as.rsi(x = as.disk(18),
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#' mo = "Strep pneu", # `mo` will be coerced with as.mo()
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#' ab = "ampicillin", # and `ab` with as.ab()
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#' guideline = "EUCAST")
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#'
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#' as.rsi(df)
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#' }
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as.disk <- function(x, na.rm = FALSE) {
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if (!is.disk(x)) {
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x <- x %>% unlist()
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if (na.rm == TRUE) {
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x <- x[!is.na(x)]
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}
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x.bak <- x
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na_before <- length(x[is.na(x)])
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# force it to be integer
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x <- suppressWarnings(as.integer(x))
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# disks can never be less than 6 mm (size of smallest disk) or more than 50 mm
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x[x < 6 | x > 50] <- NA_integer_
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na_after <- length(x[is.na(x)])
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if (na_before != na_after) {
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list_missing <- x.bak[is.na(x) & !is.na(x.bak)] %>%
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unique() %>%
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sort()
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list_missing <- paste0('"', list_missing, '"', collapse = ", ")
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warning(na_after - na_before, " results truncated (",
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round(((na_after - na_before) / length(x)) * 100),
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"%) that were invalid disk zones: ",
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list_missing, call. = FALSE)
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}
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}
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structure(as.integer(x),
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class = c("disk", "integer"))
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}
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all_valid_disks <- function(x) {
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x_disk <- suppressWarnings(as.disk(x[!is.na(x)]))
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!any(is.na(x_disk)) & !all(is.na(x))
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}
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#' @rdname as.disk
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#' @export
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is.disk <- function(x) {
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inherits(x, "disk")
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}
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#' @method print disk
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#' @export
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#' @noRd
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print.disk <- function(x, ...) {
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cat("Class <disk>\n")
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print(as.integer(x), quote = FALSE)
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}
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#' @method [ disk
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#' @export
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#' @noRd
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"[.disk" <- 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 [[ disk
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#' @export
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#' @noRd
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"[[.disk" <- 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 [<- disk
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#' @export
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#' @noRd
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"[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(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 [[<- disk
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#' @export
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#' @noRd
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"[[<-.disk" <- function(i, j, ..., value) {
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value <- as.disk(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 disk
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#' @export
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#' @noRd
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c.disk <- function(x, ...) {
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y <- NextMethod()
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y <- as.disk(y)
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attributes(y) <- attributes(x)
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y
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}
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