mirror of https://github.com/msberends/AMR.git
72 lines
1.8 KiB
R
Executable File
72 lines
1.8 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/disk.R
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\docType{data}
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\name{as.disk}
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\alias{as.disk}
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\alias{disk}
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\alias{NA_disk_}
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\alias{is.disk}
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\title{Transform Input to Disk Diffusion Diameters}
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\format{
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An object of class \code{disk} (inherits from \code{integer}) of length 1.
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}
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\usage{
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as.disk(x, na.rm = FALSE)
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NA_disk_
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is.disk(x)
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}
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\arguments{
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\item{x}{vector}
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\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
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}
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\value{
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An \link{integer} with additional class \code{\link{disk}}
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}
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\description{
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This transforms a vector to a new class \code{\link{disk}}, which is a disk diffusion growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
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}
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\details{
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Interpret disk values as SIR values with \code{\link[=as.sir]{as.sir()}}. It supports guidelines from EUCAST and CLSI.
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Disk diffusion growth zone sizes must be between 6 and 50 millimetres. Values higher than 50 but lower than 100 will be maximised to 50. All others input values outside the 6-50 range will return \code{NA}.
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\code{NA_disk_} is a missing value of the new \code{disk} class.
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}
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\examples{
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# transform existing disk zones to the `disk` class (using base R)
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df <- data.frame(
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microorganism = "Escherichia coli",
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AMP = 20,
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CIP = 14,
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GEN = 18,
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TOB = 16
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)
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df[, 2:5] <- lapply(df[, 2:5], as.disk)
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str(df)
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\donttest{
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# transforming is easier with dplyr:
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if (require("dplyr")) {
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df \%>\% mutate(across(AMP:TOB, as.disk))
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}
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}
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# interpret disk values, see ?as.sir
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as.sir(
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x = as.disk(18),
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mo = "Strep pneu", # `mo` will be coerced with as.mo()
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ab = "ampicillin", # and `ab` with as.ab()
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guideline = "EUCAST"
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)
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# interpret whole data set, pretend to be all from urinary tract infections:
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as.sir(df, uti = TRUE)
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}
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\seealso{
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\code{\link[=as.sir]{as.sir()}}
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}
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\keyword{datasets}
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