mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
72 lines
1.8 KiB
R
72 lines
1.8 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/disk.R
|
|
\docType{data}
|
|
\name{as.disk}
|
|
\alias{as.disk}
|
|
\alias{disk}
|
|
\alias{NA_disk_}
|
|
\alias{is.disk}
|
|
\title{Transform Input to Disk Diffusion Diameters}
|
|
\format{
|
|
An object of class \code{disk} (inherits from \code{integer}) of length 1.
|
|
}
|
|
\usage{
|
|
as.disk(x, na.rm = FALSE)
|
|
|
|
NA_disk_
|
|
|
|
is.disk(x)
|
|
}
|
|
\arguments{
|
|
\item{x}{vector}
|
|
|
|
\item{na.rm}{a \link{logical} indicating whether missing values should be removed}
|
|
}
|
|
\value{
|
|
An \link{integer} with additional class \code{\link{disk}}
|
|
}
|
|
\description{
|
|
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.
|
|
}
|
|
\details{
|
|
Interpret disk values as SIR values with \code{\link[=as.sir]{as.sir()}}. It supports guidelines from EUCAST and CLSI.
|
|
|
|
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}.
|
|
|
|
\code{NA_disk_} is a missing value of the new \code{disk} class.
|
|
}
|
|
\examples{
|
|
# transform existing disk zones to the `disk` class (using base R)
|
|
df <- data.frame(
|
|
microorganism = "Escherichia coli",
|
|
AMP = 20,
|
|
CIP = 14,
|
|
GEN = 18,
|
|
TOB = 16
|
|
)
|
|
df[, 2:5] <- lapply(df[, 2:5], as.disk)
|
|
str(df)
|
|
|
|
\donttest{
|
|
# transforming is easier with dplyr:
|
|
if (require("dplyr")) {
|
|
df \%>\% mutate(across(AMP:TOB, as.disk))
|
|
}
|
|
}
|
|
|
|
# interpret disk values, see ?as.sir
|
|
as.sir(
|
|
x = as.disk(18),
|
|
mo = "Strep pneu", # `mo` will be coerced with as.mo()
|
|
ab = "ampicillin", # and `ab` with as.ab()
|
|
guideline = "EUCAST"
|
|
)
|
|
|
|
# interpret whole data set, pretend to be all from urinary tract infections:
|
|
as.sir(df, uti = TRUE)
|
|
}
|
|
\seealso{
|
|
\code{\link[=as.sir]{as.sir()}}
|
|
}
|
|
\keyword{datasets}
|