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https://github.com/msberends/AMR.git
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dr. M.S. (Matthijs) Berends
179eec584f
The full rebuild of clinical_breakpoints also assigns Salmonella serovars and the Bacteroides fragilis complex correctly and adds ECOFFs for Neocosmospora solani. The rebuilt microorganisms.codes is not included, since it remaps WHONET codes that need review first.
67 lines
1.7 KiB
R
67 lines
1.7 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/disk.R
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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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\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 0 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 0 and 50 millimetres. Decimal values are rounded up. All input values outside the 0-50 range, including values higher than 50, return \code{NA} with a warning.
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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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