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107 lines
3.7 KiB
R
107 lines
3.7 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://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.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 \code{disk}, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 99.
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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 \code{\link{as.rsi}}. It supports guidelines from EUCAST and CLSI.
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#' @return Ordered integer factor with new class \code{disk}
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#' @aliases disk
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#' @export
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#' @seealso \code{\link{as.rsi}}
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # interpret disk values
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#' as.rsi(x = 12,
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' guideline = "EUCAST")
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#' as.rsi(x = 12,
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' guideline = "CLSI")
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as.disk <- function(x, na.rm = FALSE) {
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if (is.disk(x)) {
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x
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} else {
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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 9 mm (size of a disk) or more than 50 mm
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x[x < 6 | x > 99] <- 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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class(x) <- c("disk", "integer")
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x
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}
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}
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#' @rdname as.disk
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#' @export
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#' @importFrom dplyr %>%
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is.disk <- function(x) {
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class(x) %>% identical(c("disk", "integer"))
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}
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#' @exportMethod 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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#' @importFrom pillar type_sum
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#' @export
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type_sum.disk <- function(x) {
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"disk"
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}
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#' @importFrom pillar pillar_shaft
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#' @export
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pillar_shaft.disk <- function(x, ...) {
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out <- trimws(format(x))
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out[is.na(x)] <- pillar::style_na(NA)
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pillar::new_pillar_shaft_simple(out, align = "right", min_width = 3)
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}
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