AMR/R/disk.R

236 lines
7.6 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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 the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Transform input to disk diffusion diameters
#'
#' This transforms a vector to a new class [`disk`], which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres 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 class [`disk`]
#' @aliases disk
#' @export
#' @seealso [as.rsi()]
#' @inheritSection AMR Read more on our website!
#' @examples
#' \donttest{
#' # transform existing disk zones to the `disk` class
#' df <- data.frame(microorganism = "E. coli",
#' AMP = 20,
#' CIP = 14,
#' GEN = 18,
#' TOB = 16)
#' df[, 2:5] <- lapply(df[, 2:5], as.disk)
#' # same with dplyr:
#' # df %>% mutate(across(AMP:TOB, as.disk))
#'
#' # 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()
#' guideline = "EUCAST")
#'
#' as.rsi(df)
#' }
as.disk <- function(x, na.rm = FALSE) {
meet_criteria(x, allow_class = c("disk", "character", "numeric", "integer"), allow_NA = TRUE)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
if (!is.disk(x)) {
x <- x %pm>% unlist()
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}
x.bak <- x
na_before <- length(x[is.na(x)])
# heavily based on cleaner::clean_double():
clean_double2 <- function(x, remove = "[^0-9.,-]", fixed = FALSE) {
x <- gsub(",", ".", x)
# remove ending dot/comma
x <- gsub("[,.]$", "", x)
# only keep last dot/comma
reverse <- function(x) vapply(FUN.VALUE = character(1), lapply(strsplit(x, NULL), rev), paste, collapse = "")
x <- sub("{{dot}}", ".",
gsub(".", "",
reverse(sub(".", "}}tod{{",
reverse(x),
fixed = TRUE)),
fixed = TRUE),
fixed = TRUE)
x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
# remove everything that is not a number or dot
as.numeric(gsub("[^0-9.]+", "", x_clean))
}
# round up and make it an integer
x <- as.integer(ceiling(clean_double2(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)] %pm>%
unique() %pm>%
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)
}
}
set_clean_class(as.integer(x),
new_class = c("disk", "integer"))
}
all_valid_disks <- function(x) {
if (!inherits(x, c("disk", "character", "numeric", "integer"))) {
return(FALSE)
}
x_disk <- tryCatch(suppressWarnings(as.disk(x[!is.na(x)])),
error = function(e) NA)
!any(is.na(x_disk)) && !all(is.na(x))
}
#' @rdname as.disk
#' @export
is.disk <- function(x) {
inherits(x, "disk")
}
# will be exported using s3_register() in R/zzz.R
pillar_shaft.disk <- function(x, ...) {
out <- trimws(format(x))
out[is.na(x)] <- font_na(NA)
create_pillar_column(out, align = "right", width = 2)
}
# will be exported using s3_register() in R/zzz.R
type_sum.disk <- function(x, ...) {
"disk"
}
#' @method print disk
#' @export
#' @noRd
print.disk <- function(x, ...) {
cat("Class <disk>\n")
print(as.integer(x), quote = FALSE)
}
#' @method plot disk
#' @export
#' @importFrom graphics barplot axis
#' @rdname plot
plot.disk <- function(x,
main = paste("Disk zones values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Disk diffusion (mm)",
axes = FALSE,
...) {
meet_criteria(main, allow_class = "character", has_length = 1)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(axes, allow_class = "logical", has_length = 1)
barplot(table(x),
ylab = ylab,
xlab = xlab,
axes = axes,
main = main,
...)
axis(2, seq(0, max(table(x))))
}
#' @method [ disk
#' @export
#' @noRd
"[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @method [[ disk
#' @export
#' @noRd
"[[.disk" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @method [<- disk
#' @export
#' @noRd
"[<-.disk" <- function(i, j, ..., value) {
value <- as.disk(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @method [[<- disk
#' @export
#' @noRd
"[[<-.disk" <- function(i, j, ..., value) {
value <- as.disk(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @method c disk
#' @export
#' @noRd
c.disk <- function(x, ...) {
y <- NextMethod()
y <- as.disk(y)
attributes(y) <- attributes(x)
y
}
#' @method unique disk
#' @export
#' @noRd
unique.disk <- function(x, incomparables = FALSE, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
# will be exported using s3_register() in R/zzz.R
get_skimmers.disk <- function(column) {
skimr::sfl(
skim_type = "disk",
min = ~min(as.double(.), na.rm = TRUE),
max = ~max(as.double(.), na.rm = TRUE),
median = ~stats::median(as.double(.), na.rm = TRUE),
n_unique = ~pm_n_distinct(., na.rm = TRUE),
hist = ~skimr::inline_hist(stats::na.omit(as.double(.)))
)
}