mirror of
https://github.com/msberends/AMR.git
synced 2025-07-01 15:58:42 +02:00
68 lines
3.2 KiB
R
68 lines
3.2 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/random.R
|
|
\name{random}
|
|
\alias{random}
|
|
\alias{random_mic}
|
|
\alias{random_disk}
|
|
\alias{random_sir}
|
|
\title{Random MIC Values/Disk Zones/SIR Generation}
|
|
\usage{
|
|
random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
|
|
severity = 1, ...)
|
|
|
|
random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
|
|
severity = 1, ...)
|
|
|
|
random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
|
|
}
|
|
\arguments{
|
|
\item{size}{Desired size of the returned vector. If used in a \link{data.frame} call or \code{dplyr} verb, will get the current (group) size if left blank.}
|
|
|
|
\item{mo}{Any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be the same length as \code{size}.}
|
|
|
|
\item{ab}{Any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
|
|
|
|
\item{skew}{Direction of skew for MIC or disk values, either \code{"right"} or \code{"left"}. A left-skewed distribution has the majority of the data on the right.}
|
|
|
|
\item{severity}{Skew severity; higher values will increase the skewedness. Default is \code{2}; use \code{0} to prevent skewedness.}
|
|
|
|
\item{...}{Ignored, only in place to allow future extensions.}
|
|
|
|
\item{prob_SIR}{A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).}
|
|
}
|
|
\value{
|
|
class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \code{disk} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}})
|
|
}
|
|
\description{
|
|
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
|
|
}
|
|
\details{
|
|
Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the \code{skew} and \code{severity} arguments:
|
|
\itemize{
|
|
\item \code{skew = "right"} places more emphasis on lower MIC or higher disk values.
|
|
\item \code{skew = "left"} places more emphasis on higher MIC or lower disk values.
|
|
\item \code{severity} controls the exponential bias applied.
|
|
}
|
|
}
|
|
\examples{
|
|
random_mic(25)
|
|
random_disk(25)
|
|
random_sir(25)
|
|
|
|
# add more skewedness, make more realistic by setting a bug and/or drug:
|
|
disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
|
|
plot(disks)
|
|
# `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
|
|
plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")
|
|
|
|
\donttest{
|
|
random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
|
|
random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
|
|
random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
|
|
|
|
random_disk(25, "Klebsiella pneumoniae") # range 8-50
|
|
random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
|
|
random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
|
|
}
|
|
}
|