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(v1.3.0.9022) mo_matching_score(), poorman update, as.rsi() fix

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dr. M.S. (Matthijs) Berends
2020-09-18 16:05:53 +02:00
parent 89401ede9f
commit 4e40e42011
138 changed files with 2923 additions and 1472 deletions
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8
man/mdro.Rd
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@@ -59,13 +59,13 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\value{
\itemize{
\item CMI 2012 paper - function \code{\link[=mdr_cmi2012]{mdr_cmi2012()}} or \code{\link[=mdro]{mdro()}}:\cr
Ordered \code{\link{factor}} with levels \code{Negative} < \code{Multi-drug-resistant (MDR)} < \verb{Extensively drug-resistant (XDR)} < \code{Pandrug-resistant (PDR)}
Ordered \link{factor} with levels \code{Negative} < \code{Multi-drug-resistant (MDR)} < \verb{Extensively drug-resistant (XDR)} < \code{Pandrug-resistant (PDR)}
\item TB guideline - function \code{\link[=mdr_tb]{mdr_tb()}} or \code{\link[=mdro]{mdro(..., guideline = "TB")}}:\cr
Ordered \code{\link{factor}} with levels \code{Negative} < \code{Mono-resistant} < \code{Poly-resistant} < \code{Multi-drug-resistant} < \verb{Extensively drug-resistant}
Ordered \link{factor} with levels \code{Negative} < \code{Mono-resistant} < \code{Poly-resistant} < \code{Multi-drug-resistant} < \verb{Extensively drug-resistant}
\item German guideline - function \code{\link[=mrgn]{mrgn()}} or \code{\link[=mdro]{mdro(..., guideline = "MRGN")}}:\cr
Ordered \code{\link{factor}} with levels \code{Negative} < \verb{3MRGN} < \verb{4MRGN}
Ordered \link{factor} with levels \code{Negative} < \verb{3MRGN} < \verb{4MRGN}
\item Everything else:\cr
Ordered \code{\link{factor}} with levels \code{Negative} < \verb{Positive, unconfirmed} < \code{Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests
Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed} < \code{Positive}. The value \code{"Positive, unconfirmed"} means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests
}
}
\description{