mirror of https://github.com/msberends/AMR.git
327 lines
12 KiB
R
Executable File
327 lines
12 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' Class 'mic'
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#'
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#' This transforms a vector to a new class \code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
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#' @rdname as.mic
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#' @param x vector
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#' @param na.rm a logical indicating whether missing values should be removed
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#' @details Interpret MIC values as RSI values with \code{\link{as.rsi}}. It supports guidelines from EUCAST and CLSI.
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#' @return Ordered factor with new class \code{mic}
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#' @keywords mic
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#' @export
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#' @importFrom dplyr %>%
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#' @seealso \code{\link{as.rsi}}
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
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#' is.mic(mic_data)
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#'
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#' # this can also coerce combined MIC/RSI values:
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#' as.mic("<=0.002; S") # will return <=0.002
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#'
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#' # interpret MIC values
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#' as.rsi(x = as.mic(2),
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' guideline = "EUCAST")
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#' as.rsi(x = as.mic(4),
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#' mo = as.mo("S. pneumoniae"),
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#' ab = "AMX",
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#' guideline = "EUCAST")
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#'
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#' plot(mic_data)
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#' barplot(mic_data)
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#'
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#' library(clean)
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#' freq(mic_data)
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as.mic <- function(x, na.rm = FALSE) {
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if (is.mic(x)) {
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x
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} else {
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x <- x %>% unlist()
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if (na.rm == TRUE) {
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x <- x[!is.na(x)]
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}
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x.bak <- x
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# comma to period
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x <- gsub(',', '.', x, fixed = TRUE)
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# remove space between operator and number ("<= 0.002" -> "<=0.002")
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x <- gsub('(<|=|>) +', '\\1', x)
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# transform => to >= and =< to <=
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x <- gsub('=>', '>=', x, fixed = TRUE)
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x <- gsub('=<', '<=', x, fixed = TRUE)
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# starting dots must start with 0
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x <- gsub('^[.]+', '0.', x)
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# <=0.2560.512 should be 0.512
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x <- gsub('.*[.].*[.]', '0.', x)
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# remove ending .0
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x <- gsub('[.]+0$', '', x)
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# remove all after last digit
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x <- gsub('[^0-9]+$', '', x)
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# keep only one zero before dot
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x <- gsub("0+[.]", "0.", x)
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# starting 00 is probably 0.0 if there's no dot yet
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x[!x %like% "[.]"] <- gsub("^00", "0.0", x[!x %like% "[.]"])
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# remove last zeroes
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x <- gsub('([.].?)0+$', '\\1', x)
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x <- gsub('(.*[.])0+$', '\\10', x)
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# remove ending .0 again
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x[x %like% "[.]"] <- gsub('0+$', '', x[x %like% "[.]"])
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# force to be character
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x <- as.character(x)
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# trim it
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x <- trimws(x)
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## previously unempty values now empty - should return a warning later on
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x[x.bak != "" & x == ""] <- "invalid"
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# these are allowed MIC values and will become factor levels
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lvls <- c("<0.001", "<=0.001", "0.001", ">=0.001", ">0.001",
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"<0.002", "<=0.002", "0.002", ">=0.002", ">0.002",
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"<0.003", "<=0.003", "0.003", ">=0.003", ">0.003",
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"<0.004", "<=0.004", "0.004", ">=0.004", ">0.004",
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"<0.005", "<=0.005", "0.005", ">=0.005", ">0.005",
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"<0.006", "<=0.006", "0.006", ">=0.006", ">0.006",
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"<0.007", "<=0.007", "0.007", ">=0.007", ">0.007",
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"<0.008", "<=0.008", "0.008", ">=0.008", ">0.008",
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"<0.009", "<=0.009", "0.009", ">=0.009", ">0.009",
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"<0.01", "<=0.01", "0.01", ">=0.01", ">0.01",
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"<0.012", "<=0.012", "0.012", ">=0.012", ">0.012",
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"<0.0125", "<=0.0125", "0.0125", ">=0.0125", ">0.0125",
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"<0.016", "<=0.016", "0.016", ">=0.016", ">0.016",
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"<0.019", "<=0.019", "0.019", ">=0.019", ">0.019",
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"<0.02", "<=0.02", "0.02", ">=0.02", ">0.02",
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"<0.023", "<=0.023", "0.023", ">=0.023", ">0.023",
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"<0.025", "<=0.025", "0.025", ">=0.025", ">0.025",
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"<0.028", "<=0.028", "0.028", ">=0.028", ">0.028",
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"<0.03", "<=0.03", "0.03", ">=0.03", ">0.03",
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"<0.031", "<=0.031", "0.031", ">=0.031", ">0.031",
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"<0.032", "<=0.032", "0.032", ">=0.032", ">0.032",
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"<0.038", "<=0.038", "0.038", ">=0.038", ">0.038",
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"<0.04", "<=0.04", "0.04", ">=0.04", ">0.04",
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"<0.047", "<=0.047", "0.047", ">=0.047", ">0.047",
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"<0.05", "<=0.05", "0.05", ">=0.05", ">0.05",
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"<0.054", "<=0.054", "0.054", ">=0.054", ">0.054",
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"<0.06", "<=0.06", "0.06", ">=0.06", ">0.06",
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"<0.0625", "<=0.0625", "0.0625", ">=0.0625", ">0.0625",
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"<0.063", "<=0.063", "0.063", ">=0.063", ">0.063",
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"<0.064", "<=0.064", "0.064", ">=0.064", ">0.064",
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"<0.075", "<=0.075", "0.075", ">=0.075", ">0.075",
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"<0.08", "<=0.08", "0.08", ">=0.08", ">0.08",
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"<0.09", "<=0.09", "0.09", ">=0.09", ">0.09",
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"<0.094", "<=0.094", "0.094", ">=0.094", ">0.094",
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"<0.095", "<=0.095", "0.095", ">=0.095", ">0.095",
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"<0.1", "<=0.1", "0.1", ">=0.1", ">0.1",
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"<0.12", "<=0.12", "0.12", ">=0.12", ">0.12",
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"<0.125", "<=0.125", "0.125", ">=0.125", ">0.125",
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"<0.128", "<=0.128", "0.128", ">=0.128", ">0.128",
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"<0.15", "<=0.15", "0.15", ">=0.15", ">0.15",
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"<0.16", "<=0.16", "0.16", ">=0.16", ">0.16",
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"<0.17", "<=0.17", "0.17", ">=0.17", ">0.17",
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"<0.18", "<=0.18", "0.18", ">=0.18", ">0.18",
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"<0.19", "<=0.19", "0.19", ">=0.19", ">0.19",
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"<0.2", "<=0.2", "0.2", ">=0.2", ">0.2",
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"<0.23", "<=0.23", "0.23", ">=0.23", ">0.23",
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"<0.25", "<=0.25", "0.25", ">=0.25", ">0.25",
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"<0.256", "<=0.256", "0.256", ">=0.256", ">0.256",
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"<0.28", "<=0.28", "0.28", ">=0.28", ">0.28",
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"<0.3", "<=0.3", "0.3", ">=0.3", ">0.3",
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"<0.32", "<=0.32", "0.32", ">=0.32", ">0.32",
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"<0.35", "<=0.35", "0.35", ">=0.35", ">0.35",
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"<0.36", "<=0.36", "0.36", ">=0.36", ">0.36",
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"<0.38", "<=0.38", "0.38", ">=0.38", ">0.38",
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"<0.47", "<=0.47", "0.47", ">=0.47", ">0.47",
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"<0.5", "<=0.5", "0.5", ">=0.5", ">0.5",
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"<0.512", "<=0.512", "0.512", ">=0.512", ">0.512",
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"<0.64", "<=0.64", "0.64", ">=0.64", ">0.64",
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"<0.73", "<=0.73", "0.73", ">=0.73", ">0.73",
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"<0.75", "<=0.75", "0.75", ">=0.75", ">0.75",
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"<0.8", "<=0.8", "0.8", ">=0.8", ">0.8",
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"<0.94", "<=0.94", "0.94", ">=0.94", ">0.94",
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"<1", "<=1", "1", ">=1", ">1",
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"<1.5", "<=1.5", "1.5", ">=1.5", ">1.5",
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"<2", "<=2", "2", ">=2", ">2",
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"<3", "<=3", "3", ">=3", ">3",
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"<4", "<=4", "4", ">=4", ">4",
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"<5", "<=5", "5", ">=5", ">5",
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"<6", "<=6", "6", ">=6", ">6",
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"<7", "<=7", "7", ">=7", ">7",
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"<8", "<=8", "8", ">=8", ">8",
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"<10", "<=10", "10", ">=10", ">10",
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"<12", "<=12", "12", ">=12", ">12",
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"<16", "<=16", "16", ">=16", ">16",
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"<20", "<=20", "20", ">=20", ">20",
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"<24", "<=24", "24", ">=24", ">24",
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"<32", "<=32", "32", ">=32", ">32",
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"<40", "<=40", "40", ">=40", ">40",
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"<48", "<=48", "48", ">=48", ">48",
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"<64", "<=64", "64", ">=64", ">64",
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"<80", "<=80", "80", ">=80", ">80",
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"<96", "<=96", "96", ">=96", ">96",
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"<128", "<=128", "128", ">=128", ">128",
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"129",
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"<160", "<=160", "160", ">=160", ">160",
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"<256", "<=256", "256", ">=256", ">256",
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"257",
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"<320", "<=320", "320", ">=320", ">320",
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"<512", "<=512", "512", ">=512", ">512",
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"513",
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"<1024", "<=1024", "1024", ">=1024", ">1024",
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"1025")
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na_before <- x[is.na(x) | x == ''] %>% length()
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x[!x %in% lvls] <- NA
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na_after <- x[is.na(x) | x == ''] %>% length()
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if (na_before != na_after) {
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list_missing <- x.bak[is.na(x) & !is.na(x.bak) & x.bak != ''] %>%
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unique() %>%
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sort()
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list_missing <- paste0('"', list_missing , '"', collapse = ", ")
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warning(na_after - na_before, ' results truncated (',
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round(((na_after - na_before) / length(x)) * 100),
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'%) that were invalid MICs: ',
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list_missing, call. = FALSE)
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}
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structure(.Data = factor(x, levels = lvls, ordered = TRUE),
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class = c('mic', 'ordered', 'factor'))
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}
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}
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#' @rdname as.mic
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#' @export
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#' @importFrom dplyr %>%
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is.mic <- function(x) {
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class(x) %>% identical(c('mic', 'ordered', 'factor'))
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}
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#' @exportMethod as.double.mic
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#' @export
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#' @noRd
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as.double.mic <- function(x, ...) {
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as.double(gsub('(<|=|>)+', '', as.character(x)))
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}
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#' @exportMethod as.integer.mic
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#' @export
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#' @noRd
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as.integer.mic <- function(x, ...) {
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as.integer(gsub('(<|=|>)+', '', as.character(x)))
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}
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#' @exportMethod as.numeric.mic
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#' @export
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#' @noRd
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as.numeric.mic <- function(x, ...) {
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as.numeric(gsub('(<|=|>)+', '', as.character(x)))
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}
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#' @exportMethod droplevels.mic
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#' @export
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#' @noRd
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droplevels.mic <- function(x, exclude = if(anyNA(levels(x))) NULL else NA, ...) {
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x <- droplevels.factor(x, exclude = exclude, ...)
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class(x) <- c('mic', 'ordered', 'factor')
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x
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}
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#' @exportMethod print.mic
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#' @export
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#' @importFrom dplyr %>% tibble group_by summarise pull
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#' @noRd
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print.mic <- function(x, ...) {
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cat("Class 'mic'\n")
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print(as.character(x), quote = FALSE)
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}
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#' @exportMethod summary.mic
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#' @export
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#' @importFrom dplyr %>%
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#' @noRd
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summary.mic <- function(object, ...) {
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x <- object
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n_total <- x %>% length()
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x <- x[!is.na(x)]
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n <- x %>% length()
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c(
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"Class" = 'mic',
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"<NA>" = n_total - n,
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"Min." = sort(x)[1] %>% as.character(),
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"Max." = sort(x)[n] %>% as.character()
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)
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}
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#' @exportMethod plot.mic
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#' @export
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#' @importFrom graphics barplot axis par
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#' @noRd
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plot.mic <- function(x,
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main = paste('MIC values of', deparse(substitute(x))),
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ylab = 'Frequency',
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xlab = 'MIC value',
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axes = FALSE,
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...) {
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barplot(table(droplevels.factor(x)),
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ylab = ylab,
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xlab = xlab,
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axes = axes,
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main = main,
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...)
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axis(2, seq(0, max(table(droplevels.factor(x)))))
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}
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#' @exportMethod barplot.mic
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#' @export
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#' @importFrom graphics barplot axis
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#' @noRd
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barplot.mic <- function(height,
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main = paste('MIC values of', deparse(substitute(height))),
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ylab = 'Frequency',
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xlab = 'MIC value',
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axes = FALSE,
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...) {
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barplot(table(droplevels.factor(height)),
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ylab = ylab,
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xlab = xlab,
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axes = axes,
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main = main,
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...)
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axis(2, seq(0, max(table(droplevels.factor(height)))))
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}
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#' @importFrom pillar type_sum
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#' @export
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type_sum.mic <- function(x) {
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"mic"
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}
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#' @importFrom pillar pillar_shaft
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#' @export
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pillar_shaft.mic <- function(x, ...) {
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out <- trimws(format(x))
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out[is.na(x)] <- pillar::style_na(NA)
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pillar::new_pillar_shaft_simple(out, align = "right", min_width = 4)
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}
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