mirror of https://github.com/msberends/AMR.git
209 lines
6.8 KiB
R
209 lines
6.8 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Data 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 data 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 <- unlist(x)
|
|
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() %pm>%
|
|
vector_and(quotes = TRUE)
|
|
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 [ 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(...) {
|
|
as.disk(unlist(lapply(list(...), as.character)))
|
|
}
|
|
|
|
#' @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 = ~length(unique(stats::na.omit(.))),
|
|
hist = ~skimr::inline_hist(stats::na.omit(as.double(.)))
|
|
)
|
|
}
|