# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2018-2020 Berends MS, Luz CF et al. # # # # 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. # # 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 millimeters between 6 and 50. #' @inheritSection lifecycle Stable lifecycle #' @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 #' @export #' @seealso [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 6 mm (size of smallest disk) or more than 50 mm x[x < 6 | x > 50] <- 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) { inherits(x, c("disk", "integer")) } #' @exportMethod print.disk #' @export #' @noRd print.disk <- function(x, ...) { cat("Class 'disk'\n") print(as.integer(x), quote = FALSE) } #' @importFrom pillar type_sum #' @export type_sum.disk <- function(x) { "disk" } #' @importFrom pillar pillar_shaft #' @export pillar_shaft.disk <- function(x, ...) { out <- trimws(format(x)) out[is.na(x)] <- pillar::style_na(NA) pillar::new_pillar_shaft_simple(out, align = "right", min_width = 3) }