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(v0.9.0.9026) update documentation

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dr. M.S. (Matthijs) Berends
2020-02-17 14:38:01 +01:00
parent 11f00f8a0a
commit 5e2b294351
118 changed files with 997 additions and 2252 deletions
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14
man/as.rsi.Rd
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@ -23,13 +23,13 @@ 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 millimeters)}
\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{mo}{a microorganism code, generated with \code{\link[=as.mo]{as.mo()}}}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{an antimicrobial code, generated with \code{\link[=as.ab]{as.ab()}}}
\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, run \code{unique(rsi_translation$guideline)} for all options}
@ -77,7 +77,7 @@ If the unlying code needs breaking changes, they will occur gradually. To begin
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\examples{
@ -96,8 +96,10 @@ as.rsi(x = as.disk(18),
# a whole data set, even with combined MIC values and disk zones
df <- data.frame(microorganism = "E. coli",
AMP = as.mic(12),
GEN = as.disk(18))
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16))
as.rsi(df)