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(v1.8.1.9009) random when pkg not loaded

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dr. M.S. (Matthijs) Berends
2022-05-16 09:29:46 +02:00
parent 58ed15e7ac
commit 2c5bc73ed6
28 changed files with 121 additions and 78 deletions
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2
man/as.rsi.Rd
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@ -68,7 +68,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}

2
man/g.test.Rd
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@ -21,7 +21,7 @@ g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)
\item{y}{a numeric vector; ignored if \code{x} is a matrix. If
\code{x} is a factor, \code{y} should be a factor of the same length.}
\item{p}{a vector of probabilities of the same length of \code{x}.
\item{p}{a vector of probabilities of the same length as \code{x}.
An error is given if any entry of \code{p} is negative.}
\item{rescale.p}{a logical scalar; if TRUE then \code{p} is rescaled

2
man/random.Rd
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@ -33,7 +33,7 @@ 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 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} argument.
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.
}
\section{Stable Lifecycle}{

17
man/rsi_translation.Rd
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@ -27,6 +27,23 @@ rsi_translation
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
Overview of the data set:\if{html}{\out{<div class="sourceCode r">}}\preformatted{head(rsi_translation)
}\if{html}{\out{</div>}}\preformatted{## guideline method site mo rank_index ab ref_tbl disk_dose
## 1 EUCAST 2022 MIC <NA> F_ASPRG_MGTS 2 AMB Aspergillus <NA>
## 2 EUCAST 2022 MIC <NA> F_ASPRG_NIGR 2 AMB Aspergillus <NA>
## 3 EUCAST 2022 MIC <NA> F_CANDD 3 AMB Candida <NA>
## 4 EUCAST 2022 MIC <NA> F_CANDD_ALBC 2 AMB Candida <NA>
## 5 EUCAST 2022 MIC <NA> F_CANDD_DBLN 2 AMB Candida <NA>
## 6 EUCAST 2022 MIC <NA> F_CANDD_KRUS 2 AMB Candida <NA>
## breakpoint_S breakpoint_R uti
## 1 1 1 FALSE
## 2 1 1 FALSE
## 3 1 1 FALSE
## 4 1 1 FALSE
## 5 1 1 FALSE
## 6 1 1 FALSE
}
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.
}
\section{Reference Data Publicly Available}{