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(v0.7.1.9035) cephalosporins and unit tests

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dr. M.S. (Matthijs) Berends
2019-08-11 19:07:26 +02:00
parent 3f5828e74a
commit 1d423cca89
38 changed files with 382 additions and 361 deletions
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6
man/as.rsi.Rd
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@ -29,13 +29,13 @@ is.rsi.eligible(x, threshold = 0.05)
\item{mo}{a microorganism code, generated with \code{\link{as.mo}}}
\item{ab}{an antibiotic code, generated with \code{\link{as.ab}}}
\item{ab}{an antimicrobial code, generated with \code{\link{as.ab}}}
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see Examples}
}
\value{
Ordered factor with new class \code{rsi}
@ -46,7 +46,7 @@ Interpret MIC values according to EUCAST or CLSI, or clean up existing RSI value
\details{
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.
After using \code{as.rsi}, you can use \code{\link{eucast_rules}} to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
After using \code{as.rsi}, you can use \code{\link{eucast_rules}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter.
}