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(v1.4.0.9037) random_* functions

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dr. M.S. (Matthijs) Berends
2020-12-12 23:17:29 +01:00
parent 2edd3339db
commit c8bcecf232
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10
man/is_new_episode.Rd
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@ -22,12 +22,16 @@ This function determines which items in a vector can be considered (the start of
\details{
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least \code{episode_days} days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least \code{episode_days} days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
The \code{dplyr} package is not required for this function to work, but this function works conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
}
\section{Experimental lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_experimental.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{experimental}. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this \code{AMR} package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
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.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an 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.
}
\section{Read more on our website!}{

12
man/plot.Rd
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@ -1,13 +1,23 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/amr.R, R/mic.R, R/rsi.R
% Please edit documentation in R/amr.R, R/disk.R, R/mic.R, R/rsi.R
\name{plot}
\alias{plot}
\alias{plot.disk}
\alias{plot.mic}
\alias{barplot.mic}
\alias{plot.rsi}
\alias{barplot.rsi}
\title{Plotting for classes \code{rsi} and \code{disk}}
\usage{
\method{plot}{disk}(
x,
main = paste("Disk zones values of", deparse(substitute(x))),
ylab = "Frequency",
xlab = "Disk diffusion (mm)",
axes = FALSE,
...
)
\method{plot}{mic}(
x,
main = paste("MIC values of", deparse(substitute(x))),

64
man/random.Rd Normal file
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@ -0,0 +1,64 @@
% 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_rsi}
\title{Random MIC values/disk zones/RSI generation}
\usage{
random_mic(size, mo = NULL, ab = NULL, ...)
random_disk(size, mo = NULL, ab = NULL, ...)
random_rsi(size, prob_RSI = c(0.33, 0.33, 0.33), ...)
}
\arguments{
\item{size}{desired size of the returned vector}
\item{mo}{any character that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{any character that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}}
\item{...}{extension for future versions, not used at the moment}
\item{prob_RSI}{a vector of length 3: the probabilities for R (1st value), S (2nd value) and I (3rd value)}
}
\value{
class \verb{<mic>} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \verb{<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 analysis practice.
}
\details{
The base R function \code{\link[=sample]{sample()}} is used for generating values.
Generated values are based on the latest EUCAST guideline 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} parameter.
}
\section{Maturing lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. Since this function needs wider usage and more extensive testing, you are very welcome \href{https://github.com/msberends/AMR/issues}{to suggest changes at our repository} or \link[=AMR]{write us an email (see section 'Contact Us')}.
}
\section{Read more on our website!}{
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 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}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{
random_mic(100)
random_disk(100)
random_rsi(100)
\donttest{
# make the random generation more realistic by setting a bug and/or drug:
random_mic(100, "Klebsiella pneumoniae") # range 0.0625-64
random_mic(100, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
random_mic(100, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
random_disk(100, "Klebsiella pneumoniae") # range 11-50
random_disk(100, "Klebsiella pneumoniae", "ampicillin") # range 6-14
random_disk(100, "Streptococcus pneumoniae", "ampicillin") # range 16-22
}
}