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AMR/R/rsi.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# #
# This R package was created for academic research and 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 'rsi'
#'
#' This transforms a vector to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
#' @rdname as.rsi
#' @param x vector
#' @param threshold maximum fraction of \code{x} that is allowed to fail transformation, see Examples
#' @details The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
#' @return Ordered factor with new class \code{rsi}
#' @keywords rsi
#' @export
#' @importFrom dplyr %>%
#' @seealso \code{\link{as.mic}}
#' @inheritSection AMR Read more on our website!
#' @examples
#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
#' rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
#' is.rsi(rsi_data)
#'
#' # this can also coerce combined MIC/RSI values:
#' as.rsi("<= 0.002; S") # will return S
#'
#' plot(rsi_data) # for percentages
#' barplot(rsi_data) # for frequencies
#' freq(rsi_data) # frequency table with informative header
#'
#' # using dplyr's mutate
#' library(dplyr)
#' septic_patients %>%
#' mutate_at(vars(peni:rifa), as.rsi)
#'
#'
#' # fastest way to transform all columns with already valid AB results to class `rsi`:
#' septic_patients %>%
#' mutate_if(is.rsi.eligible,
#' as.rsi)
#'
#' # default threshold of `is.rsi.eligible` is 5%.
#' is.rsi.eligible(WHONET$`First name`) # fails, >80% is invalid
#' is.rsi.eligible(WHONET$`First name`, threshold = 0.9) # succeeds
as.rsi <- function(x) {
if (is.rsi(x)) {
x
} else if (identical(levels(x), c("S", "I", "R"))) {
structure(x, class = c('rsi', 'ordered', 'factor'))
} else {
if (mic_like(x) > 0.5) {
warning("`as.rsi` is intended to clean antimicrobial interpretations - not to interpret MIC values.", call. = FALSE)
}
x <- x %>% unlist()
x.bak <- x
na_before <- x[is.na(x) | x == ''] %>% length()
# remove all spaces
x <- gsub(' +', '', x)
# remove all MIC-like values: numbers, operators and periods
x <- gsub('[0-9.,;:<=>]+', '', x)
# remove everything between brackets, and 'high' and 'low'
x <- gsub("([(].*[)])", "", x)
x <- gsub("(high|low)", "", x, ignore.case = TRUE)
# disallow more than 3 characters
x[nchar(x) > 3] <- NA
# set to capitals
x <- toupper(x)
# remove all invalid characters
x <- gsub('[^RSI]+', '', x)
# in cases of "S;S" keep S, but in case of "S;I" make it NA
x <- gsub('^S+$', 'S', x)
x <- gsub('^I+$', 'I', x)
x <- gsub('^R+$', 'R', x)
x[!x %in% c('S', 'I', 'R')] <- 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 antimicrobial interpretations: ',
list_missing, call. = FALSE)
}
x <- factor(x, levels = c("S", "I", "R"), ordered = TRUE)
class(x) <- c('rsi', 'ordered', 'factor')
x
}
}
mic_like <- function(x) {
mic <- x %>%
gsub("[^0-9.,]+", "", .) %>%
unique()
mic_valid <- suppressWarnings(as.mic(mic))
result <- sum(!is.na(mic_valid)) / length(mic)
if (is.na(result)) {
0
} else {
result
}
}
#' @rdname as.rsi
#' @export
is.rsi <- function(x) {
identical(class(x),
c('rsi', 'ordered', 'factor'))
}
#' @rdname as.rsi
#' @export
is.rsi.eligible <- function(x, threshold = 0.05) {
if (NCOL(x) > 1) {
stop('`x` must be a one-dimensional vector.')
}
if (any(c("logical",
"numeric",
"integer",
"mo",
"Date",
"POSIXct",
"rsi",
"raw",
"hms")
%in% class(x))) {
# no transformation needed
FALSE
} else {
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
if (length(x) == 0) {
return(FALSE)
}
checked <- suppressWarnings(as.rsi(x))
outcome <- sum(is.na(checked)) / length(x)
outcome <= threshold
}
}
#' @exportMethod print.rsi
#' @export
#' @importFrom dplyr %>%
#' @noRd
print.rsi <- function(x, ...) {
cat("Class 'rsi'\n")
print(as.character(x), quote = FALSE)
}
#' @exportMethod droplevels.rsi
#' @export
#' @noRd
droplevels.rsi <- function(x, exclude = if(anyNA(levels(x))) NULL else NA, ...) {
x <- droplevels.factor(x, exclude = exclude, ...)
class(x) <- c('rsi', 'ordered', 'factor')
x
}
#' @exportMethod summary.rsi
#' @export
#' @noRd
summary.rsi <- function(object, ...) {
x <- object
c(
"Class" = 'rsi',
"<NA>" = sum(is.na(x)),
"Sum S" = sum(x == "S", na.rm = TRUE),
"Sum IR" = sum(x %in% c("I", "R"), na.rm = TRUE),
"-Sum R" = sum(x == "R", na.rm = TRUE),
"-Sum I" = sum(x == "I", na.rm = TRUE)
)
}
#' @exportMethod plot.rsi
#' @export
#' @importFrom dplyr %>% group_by summarise filter mutate if_else n_distinct
#' @importFrom graphics plot text
#' @noRd
plot.rsi <- function(x, ...) {
x_name <- deparse(substitute(x))
suppressWarnings(
data <- data.frame(x = x,
y = 1,
stringsAsFactors = TRUE) %>%
group_by(x) %>%
summarise(n = sum(y)) %>%
filter(!is.na(x)) %>%
mutate(s = round((n / sum(n)) * 100, 1))
)
data$x <- factor(data$x, levels = c('S', 'I', 'R'), ordered = TRUE)
ymax <- if_else(max(data$s) > 95, 105, 100)
plot(x = data$x,
y = data$s,
lwd = 2,
col = c('green', 'orange', 'red'),
ylim = c(0, ymax),
ylab = 'Percentage',
xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibility Analysis of', x_name),
axes = FALSE,
...)
# x axis
axis(side = 1, at = 1:n_distinct(data$x), labels = levels(data$x), lwd = 0)
# y axis, 0-100%
axis(side = 2, at = seq(0, 100, 5))
text(x = data$x,
y = data$s + 4,
labels = paste0(data$s, '% (n = ', data$n, ')'))
}
#' @exportMethod barplot.rsi
#' @export
#' @importFrom dplyr %>% group_by summarise filter mutate if_else n_distinct
#' @importFrom graphics barplot axis
#' @noRd
barplot.rsi <- function(height, ...) {
x <- height
x_name <- deparse(substitute(height))
suppressWarnings(
data <- data.frame(rsi = x, cnt = 1) %>%
group_by(rsi) %>%
summarise(cnt = sum(cnt)) %>%
droplevels()
)
barplot(table(x),
col = c('green3', 'orange2', 'red3'),
xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibility Analysis of', x_name),
ylab = 'Frequency',
axes = FALSE,
...)
# y axis, 0-100%
axis(side = 2, at = seq(0, max(data$cnt) + max(data$cnt) * 1.1, by = 25))
}