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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Class 'disk'
#'
#' This transforms a vector to a new class \code{disk}, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99.
#' @rdname as.disk
#' @param x vector
#' @param na.rm a logical indicating whether missing values should be removed
#' @details Interpret disk values as RSI values with \code{\link{as.rsi}}. It supports guidelines from EUCAST and CLSI.
#' @return Ordered integer factor with new class \code{disk}
#' @keywords disk
#' @export
#' @seealso \code{\link{as.rsi}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' # interpret disk values
#' as.rsi(x = 12,
#' mo = as.mo("S. pneumoniae"),
#' ab = "AMX",
#' guideline = "EUCAST")
#' as.rsi(x = 12,
#' mo = as.mo("S. pneumoniae"),
#' ab = "AMX",
#' guideline = "CLSI")
as.disk <- function(x, na.rm = FALSE) {
if (is.disk(x)) {
x
} else {
x <- x %>% unlist()
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}
x.bak <- x
na_before <- length(x[is.na(x)])
# force it to be integer
x <- suppressWarnings(as.integer(x))
# disks can never be less than 9 mm (size of a disk) or more than 50 mm
x[x < 6 | x > 99] <- NA_integer_
na_after <- length(x[is.na(x)])
if (na_before != na_after) {
list_missing <- x.bak[is.na(x) & !is.na(x.bak)] %>%
unique() %>%
sort()
list_missing <- paste0('"', list_missing , '"', collapse = ", ")
warning(na_after - na_before, ' results truncated (',
round(((na_after - na_before) / length(x)) * 100),
'%) that were invalid disk zones: ',
list_missing, call. = FALSE)
}
class(x) <- c('disk', 'integer')
x
}
}
#' @rdname as.disk
#' @export
#' @importFrom dplyr %>%
is.disk <- function(x) {
class(x) %>% identical(c('disk', 'integer'))
}
#' @exportMethod print.disk
#' @export
#' @noRd
print.disk <- function(x, ...) {
cat("Class 'disk'\n")
print(as.integer(x), quote = FALSE)
}