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AMR/R/mic.R

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# ==================================================================== #
# 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)
# transform Unicode for >= and <=
x <- gsub("\u2264", "<=", x, fixed = TRUE)
x <- gsub("\u2265", ">=", 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)
# values like "<=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+$", "", x[x %like% "[.]"])
# never end with dot
x <- gsub("[.]$", "", x)
# 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"))
}
}
all_valid_mics <- function(x) {
x_mic <- suppressWarnings(as.mic(x[!is.na(x)]))
!any(is.na(x_mic)) & !all(is.na(x))
}
#' @rdname as.mic
#' @export
#' @importFrom dplyr %>%
is.mic <- function(x) {
inherits(x, "mic")
}
#' @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 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)
}
#' @exportMethod [.mic
#' @export
#' @noRd
"[.mic" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [[.mic
#' @export
#' @noRd
"[[.mic" <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
#' @exportMethod [<-.mic
#' @export
#' @noRd
"[<-.mic" <- function(i, j, ..., value) {
value <- as.mic(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @exportMethod [[<-.mic
#' @export
#' @noRd
"[[<-.mic" <- function(i, j, ..., value) {
value <- as.mic(value)
y <- NextMethod()
attributes(y) <- attributes(i)
y
}
#' @exportMethod c.mic
#' @export
#' @noRd
c.mic <- function(x, ...) {
y <- NextMethod()
attributes(y) <- attributes(x)
y
}
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