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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
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man/as.disk.Rd
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@ -19,7 +19,7 @@ is.disk(x)
An \code{\link{integer}} with additional new class \code{\link{disk}}
}
\description{
This transforms a vector to a new class \code{\link{disk}}, which is a growth zone size (around an antibiotic disk) in millimeters between 6 and 50.
This transforms a vector to a new class \code{\link{disk}}, which is a growth zone size (around an antibiotic disk) in millimetres between 6 and 50.
}
\details{
Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It supports guidelines from EUCAST and CLSI.
@ -34,19 +34,26 @@ 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{
# interpret disk values
as.rsi(x = 12,
mo = as.mo("S. pneumoniae"),
ab = "AMX",
# transform existing disk zones to the `disk` class
df <- data.frame(microorganism = "E. coli",
AMP = 20,
CIP = 14,
GEN = 18,
TOB = 16)
df <- df \%>\% mutate_at(vars(AMP:TOB, as.disk))
df
# interpret disk values, see ?as.rsi
as.rsi(x = as.disk(18),
mo = "Strep pneu", # `mo` will be coerced with as.mo()
ab = "ampicillin", # and `ab` with as.ab()
guideline = "EUCAST")
as.rsi(x = 12,
mo = as.mo("S. pneumoniae"),
ab = "AMX",
guideline = "CLSI")
as.rsi(df)
}
\seealso{
\code{\link[=as.rsi]{as.rsi()}}