mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
243 lines
8.1 KiB
R
Executable File
243 lines
8.1 KiB
R
Executable File
# ==================================================================== #
|
|
# 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 'mic'
|
|
#'
|
|
#' This transforms a vector to a new class [`mic`], which is an ordered [`factor`] with valid MIC values as levels. Invalid MIC values will be translated as `NA` with a warning.
|
|
#' @inheritSection lifecycle Stable lifecycle
|
|
#' @rdname as.mic
|
|
#' @param x vector
|
|
#' @param na.rm a logical indicating whether missing values should be removed
|
|
#' @details To interpret MIC values as RSI values, use [as.rsi()] on MIC values. It supports guidelines from EUCAST and CLSI.
|
|
#' @return Ordered [`factor`] with new class [`mic`]
|
|
#' @aliases mic
|
|
#' @export
|
|
#' @importFrom dplyr %>%
|
|
#' @seealso [as.rsi()]
|
|
#' @inheritSection AMR Read more on our website!
|
|
#' @examples
|
|
#' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
|
|
#' is.mic(mic_data)
|
|
#'
|
|
#' # this can also coerce combined MIC/RSI values:
|
|
#' as.mic("<=0.002; S") # will return <=0.002
|
|
#'
|
|
#' # interpret MIC values
|
|
#' as.rsi(x = as.mic(2),
|
|
#' mo = as.mo("S. pneumoniae"),
|
|
#' ab = "AMX",
|
|
#' guideline = "EUCAST")
|
|
#' as.rsi(x = as.mic(4),
|
|
#' mo = as.mo("S. pneumoniae"),
|
|
#' ab = "AMX",
|
|
#' guideline = "EUCAST")
|
|
#'
|
|
#' plot(mic_data)
|
|
#' barplot(mic_data)
|
|
#' freq(mic_data)
|
|
as.mic <- function(x, na.rm = FALSE) {
|
|
if (is.mic(x)) {
|
|
x
|
|
} else {
|
|
x <- x %>% unlist()
|
|
if (na.rm == TRUE) {
|
|
x <- x[!is.na(x)]
|
|
}
|
|
x.bak <- x
|
|
|
|
# comma to period
|
|
x <- gsub(",", ".", x, fixed = TRUE)
|
|
# remove space between operator and number ("<= 0.002" -> "<=0.002")
|
|
x <- gsub("(<|=|>) +", "\\1", x)
|
|
# transform => to >= and =< to <=
|
|
x <- gsub("=>", ">=", x, fixed = TRUE)
|
|
x <- gsub("=<", "<=", x, fixed = TRUE)
|
|
# starting dots must start with 0
|
|
x <- gsub("^[.]+", "0.", x)
|
|
# <=0.2560.512 should be 0.512
|
|
x <- gsub(".*[.].*[.]", "0.", x)
|
|
# remove ending .0
|
|
x <- gsub("[.]+0$", "", x)
|
|
# remove all after last digit
|
|
x <- gsub("[^0-9]+$", "", x)
|
|
# keep only one zero before dot
|
|
x <- gsub("0+[.]", "0.", x)
|
|
# starting 00 is probably 0.0 if there's no dot yet
|
|
x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
|
|
# remove last zeroes
|
|
x <- gsub("([.].?)0+$", "\\1", x)
|
|
x <- gsub("(.*[.])0+$", "\\10", x)
|
|
# remove ending .0 again
|
|
x[x %like% "[.]"] <- gsub("0+$", "", x[x %like% "[.]"])
|
|
# force to be character
|
|
x <- as.character(x)
|
|
# trim it
|
|
x <- trimws(x)
|
|
|
|
## previously unempty values now empty - should return a warning later on
|
|
x[x.bak != "" & x == ""] <- "invalid"
|
|
|
|
# these are allowed MIC values and will become factor levels
|
|
ops <- c("<", "<=", "", ">=", ">")
|
|
lvls <- c(c(t(sapply(ops, function(x) paste0(x, "0.00", 1:9)))),
|
|
unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.0",
|
|
sort(c(1:99, 125, 128, 256, 512, 625)))))))))),
|
|
unique(c(t(sapply(ops, function(x) paste0(x, sort(as.double(paste0("0.",
|
|
c(1:99, 125, 128, 256, 512))))))))),
|
|
c(t(sapply(ops, function(x) paste0(x, sort(c(1:9, 1.5)))))),
|
|
c(t(sapply(ops, function(x) paste0(x, c(10:98)[9:98 %% 2 == TRUE])))),
|
|
c(t(sapply(ops, function(x) paste0(x, sort(c(2 ^ c(7:10), 80 * c(2:12))))))))
|
|
|
|
na_before <- x[is.na(x) | x == ""] %>% length()
|
|
x[!x %in% lvls] <- NA
|
|
na_after <- x[is.na(x) | x == ""] %>% length()
|
|
|
|
if (na_before != na_after) {
|
|
list_missing <- x.bak[is.na(x) & !is.na(x.bak) & 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 MICs: ",
|
|
list_missing, call. = FALSE)
|
|
}
|
|
|
|
structure(.Data = factor(x, levels = lvls, ordered = TRUE),
|
|
class = c("mic", "ordered", "factor"))
|
|
}
|
|
}
|
|
|
|
#' @rdname as.mic
|
|
#' @export
|
|
#' @importFrom dplyr %>%
|
|
is.mic <- function(x) {
|
|
class(x) %>% identical(c("mic", "ordered", "factor"))
|
|
}
|
|
|
|
#' @exportMethod as.double.mic
|
|
#' @export
|
|
#' @noRd
|
|
as.double.mic <- function(x, ...) {
|
|
as.double(gsub("(<|=|>)+", "", as.character(x)))
|
|
}
|
|
|
|
#' @exportMethod as.integer.mic
|
|
#' @export
|
|
#' @noRd
|
|
as.integer.mic <- function(x, ...) {
|
|
as.integer(gsub("(<|=|>)+", "", as.character(x)))
|
|
}
|
|
|
|
#' @exportMethod as.numeric.mic
|
|
#' @export
|
|
#' @noRd
|
|
as.numeric.mic <- function(x, ...) {
|
|
as.numeric(gsub("(<|=|>)+", "", as.character(x)))
|
|
}
|
|
|
|
#' @exportMethod droplevels.mic
|
|
#' @export
|
|
#' @noRd
|
|
droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) {
|
|
x <- droplevels.factor(x, exclude = exclude, ...)
|
|
class(x) <- c("mic", "ordered", "factor")
|
|
x
|
|
}
|
|
|
|
#' @exportMethod print.mic
|
|
#' @export
|
|
#' @importFrom dplyr %>% tibble group_by summarise pull
|
|
#' @noRd
|
|
print.mic <- function(x, ...) {
|
|
cat("Class 'mic'\n")
|
|
print(as.character(x), quote = FALSE)
|
|
}
|
|
|
|
#' @exportMethod summary.mic
|
|
#' @export
|
|
#' @importFrom dplyr %>%
|
|
#' @noRd
|
|
summary.mic <- function(object, ...) {
|
|
x <- object
|
|
n_total <- x %>% length()
|
|
x <- x[!is.na(x)]
|
|
n <- x %>% length()
|
|
c(
|
|
"Class" = "mic",
|
|
"<NA>" = n_total - n,
|
|
"Min." = sort(x)[1] %>% as.character(),
|
|
"Max." = sort(x)[n] %>% as.character()
|
|
)
|
|
}
|
|
|
|
#' @exportMethod plot.mic
|
|
#' @export
|
|
#' @importFrom graphics barplot axis par
|
|
#' @noRd
|
|
plot.mic <- function(x,
|
|
main = paste("MIC values of", deparse(substitute(x))),
|
|
ylab = "Frequency",
|
|
xlab = "MIC value",
|
|
axes = FALSE,
|
|
...) {
|
|
barplot(table(droplevels.factor(x)),
|
|
ylab = ylab,
|
|
xlab = xlab,
|
|
axes = axes,
|
|
main = main,
|
|
...)
|
|
axis(2, seq(0, max(table(droplevels.factor(x)))))
|
|
}
|
|
|
|
#' @exportMethod barplot.mic
|
|
#' @export
|
|
#' @importFrom graphics barplot axis
|
|
#' @noRd
|
|
barplot.mic <- function(height,
|
|
main = paste("MIC values of", deparse(substitute(height))),
|
|
ylab = "Frequency",
|
|
xlab = "MIC value",
|
|
axes = FALSE,
|
|
...) {
|
|
barplot(table(droplevels.factor(height)),
|
|
ylab = ylab,
|
|
xlab = xlab,
|
|
axes = axes,
|
|
main = main,
|
|
...)
|
|
axis(2, seq(0, max(table(droplevels.factor(height)))))
|
|
}
|
|
|
|
#' @importFrom pillar type_sum
|
|
#' @export
|
|
type_sum.mic <- function(x) {
|
|
"mic"
|
|
}
|
|
|
|
#' @importFrom pillar pillar_shaft
|
|
#' @export
|
|
pillar_shaft.mic <- function(x, ...) {
|
|
out <- trimws(format(x))
|
|
out[is.na(x)] <- pillar::style_na(NA)
|
|
pillar::new_pillar_shaft_simple(out, align = "right", min_width = 4)
|
|
}
|