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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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12
man/random.Rd
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@ -4,14 +4,14 @@
\alias{random}
\alias{random_mic}
\alias{random_disk}
\alias{random_rsi}
\title{Random MIC Values/Disk Zones/RSI Generation}
\alias{random_sir}
\title{Random MIC Values/Disk Zones/SIR Generation}
\usage{
random_mic(size = NULL, mo = NULL, ab = NULL, ...)
random_disk(size = NULL, mo = NULL, ab = NULL, ...)
random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
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.}
@ -22,7 +22,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
\item{...}{ignored, only in place to allow future extensions}
\item{prob_RSI}{a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)}
\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()}})
@ -33,12 +33,12 @@ These functions can be used for generating random MIC values and disk diffusion
\details{
The base \R function \code{\link[=sample]{sample()}} is used for generating values.
Generated values are based on the EUCAST 2022 guideline as implemented in the \link{rsi_translation} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
Generated values are based on the EUCAST 2022 guideline as implemented 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.
}
\examples{
random_mic(25)
random_disk(25)
random_rsi(25)
random_sir(25)
\donttest{
# make the random generation more realistic by setting a bug and/or drug: