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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
# 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. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Class 'disk'
#'
#' 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.
#' @inheritSection lifecycle Stable lifecycle
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#' @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 [as.rsi()]. It supports guidelines from EUCAST and CLSI.
#' @return An [`integer`] with additional new class [`disk`]
#' @aliases disk
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#' @export
#' @seealso [as.rsi()]
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#' @inheritSection AMR Read more on our website!
#' @examples
#' \dontrun{
#' # transform existing disk zones to the `disk` class
#' library(dplyr)
#' df <- data.frame(microorganism = "E. coli",
#' AMP = 20,
#' CIP = 14,
#' GEN = 18,
#' TOB = 16)
#' df <- df %>% mutate_at(vars(AMP:TOB), as.disk)
#' df
#'
#' # interpret disk values, see ?as.rsi
#' as.rsi(x = as.disk(18),
#' mo = "Strep pneu", # `mo` will be coerced with as.mo()
#' ab = "ampicillin", # and `ab` with as.ab()
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#' guideline = "EUCAST")
#'
#' as.rsi(df)
#' }
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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 6 mm (size of smallest disk) or more than 50 mm
x[x < 6 | x > 50] <- NA_integer_
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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 (",
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round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
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list_missing, call. = FALSE)
}
class(x) <- "disk"
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x
}
}
all_valid_disks <- function(x) {
x_disk <- suppressWarnings(as.disk(x[!is.na(x)]))
!any(is.na(x_disk)) & !all(is.na(x))
}
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#' @rdname as.disk
#' @export
is.disk <- function(x) {
inherits(x, "disk")
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}
#' @exportMethod as.data.frame.disk
#' @export
#' @noRd
as.data.frame.disk <- function(x, ...) {
# same as as.data.frame.integer but with removed stringsAsFactors, since it will be class "disk"
nm <- paste(deparse(substitute(x), width.cutoff = 500L),
collapse = " ")
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(x, ..., nm = nm)
} else {
as.data.frame.vector(x, ...)
}
}
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#' @exportMethod print.disk
#' @export
#' @noRd
print.disk <- function(x, ...) {
cat("Class 'disk'\n")
print(as.integer(x), quote = FALSE)
}
#' @importFrom pillar pillar_shaft
#' @export
pillar_shaft.disk <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_red(NA)
pillar::new_pillar_shaft_simple(out, align = "right", min_width = 3)
}
#' @exportMethod [.disk
#' @export
#' @noRd
"[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.disk
#' @export
#' @noRd
"[[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.disk
#' @export
#' @noRd
"[<-.disk" <- function(i, j, ..., value) {
value <- as.disk(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @exportMethod [[<-.disk
#' @export
#' @noRd
"[[<-.disk" <- function(i, j, ..., value) {
value <- as.disk(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @exportMethod c.disk
#' @export
#' @noRd
c.disk <- function(x, ...) {
y <- NextMethod()
y <- as.disk(y)
attributes(y) <- attributes(x)
y
}