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(v1.3.0) v1.3.0

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dr. M.S. (Matthijs) Berends
2020-07-29 13:48:50 +02:00
parent de0f7b8950
commit ea4e5e5b81
15 changed files with 68 additions and 73 deletions
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16
man/as.rsi.Rd
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@ -3,15 +3,19 @@
\name{as.rsi}
\alias{as.rsi}
\alias{rsi}
\alias{is.rsi}
\alias{is.rsi.eligible}
\alias{as.rsi.mic}
\alias{as.rsi.disk}
\alias{as.rsi.data.frame}
\alias{is.rsi}
\alias{is.rsi.eligible}
\title{Class 'rsi'}
\usage{
as.rsi(x, ...)
is.rsi(x)
is.rsi.eligible(x, threshold = 0.05)
\method{as.rsi}{mic}(
x,
mo,
@ -39,16 +43,14 @@ as.rsi(x, ...)
conserve_capped_values = FALSE,
...
)
is.rsi(x)
is.rsi.eligible(x, threshold = 0.05)
}
\arguments{
\item{x}{vector of values (for class \code{\link{mic}}: an MIC value in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres)}
\item{...}{parameters passed on to methods}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
@ -60,8 +62,6 @@ is.rsi.eligible(x, threshold = 0.05)
\item{conserve_capped_values}{a logical to indicate that MIC values starting with \code{">"} (but not \code{">="}) must always return "R" , and that MIC values starting with \code{"<"} (but not \code{"<="}) must always return "S"}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, please see \emph{Examples}}
}
\value{
Ordered factor with new class \code{\link{rsi}}