mirror of https://github.com/msberends/AMR.git
54 lines
2.3 KiB
R
54 lines
2.3 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/random.R
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\name{random}
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\alias{random}
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\alias{random_mic}
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\alias{random_disk}
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\alias{random_sir}
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\title{Random MIC Values/Disk Zones/SIR Generation}
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\usage{
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random_mic(size = NULL, mo = NULL, ab = NULL, ...)
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random_disk(size = NULL, mo = NULL, ab = NULL, ...)
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random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
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}
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\arguments{
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\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.}
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\item{mo}{any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
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\item{ab}{any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{...}{ignored, only in place to allow future extensions}
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\item{prob_SIR}{a vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value)}
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}
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\value{
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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()}})
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}
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\description{
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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.
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}
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\details{
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The base \R function \code{\link[=sample]{sample()}} is used for generating values.
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Generated values are based on the EUCAST 2023 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.
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}
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\examples{
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random_mic(25)
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random_disk(25)
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random_sir(25)
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\donttest{
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# make the random generation more realistic by setting a bug and/or drug:
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random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
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random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
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random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
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random_disk(25, "Klebsiella pneumoniae") # range 8-50
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random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
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random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
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}
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}
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