mirror of https://github.com/msberends/AMR.git
74 lines
2.6 KiB
R
74 lines
2.6 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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\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 RSI values with \code{\link[=as.rsi]{as.rsi()}}. It supports guidelines from EUCAST and CLSI.
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\code{NA_disk_} is a missing value of the new \verb{<disk>} class.
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}
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\section{Stable Lifecycle}{
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\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:"5"} \cr}
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The \link[=lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
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If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
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}
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\section{Read more on Our Website!}{
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On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\examples{
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\donttest{
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# transform existing disk zones to the `disk` class
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df <- data.frame(microorganism = "E. 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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df[, 2:5] <- lapply(df[, 2:5], as.disk)
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# same with dplyr:
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# df \%>\% mutate(across(AMP:TOB, as.disk))
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# interpret disk values, see ?as.rsi
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as.rsi(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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as.rsi(df)
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}
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}
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\seealso{
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\code{\link[=as.rsi]{as.rsi()}}
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}
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\keyword{datasets}
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