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(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

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dr. M.S. (Matthijs) Berends
2021-02-02 23:57:35 +01:00
parent 20d638c193
commit 2eca8c3f01
246 changed files with 1171 additions and 965 deletions
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20
man/mdro.Rd
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@ -27,20 +27,26 @@ mdro(
pct_required_classes = 0.5,
combine_SI = TRUE,
verbose = FALSE,
only_rsi_columns = any(is.rsi(x)),
...
)
custom_mdro_guideline(..., as_factor = TRUE)
brmo(x, guideline = "BRMO", ...)
brmo(x, guideline = "BRMO", only_rsi_columns = any(is.rsi(x)), ...)
mrgn(x, guideline = "MRGN", ...)
mrgn(x, guideline = "MRGN", only_rsi_columns = any(is.rsi(x)), ...)
mdr_tb(x, guideline = "TB", ...)
mdr_tb(x, guideline = "TB", only_rsi_columns = any(is.rsi(x)), ...)
mdr_cmi2012(x, guideline = "CMI2012", ...)
mdr_cmi2012(x, guideline = "CMI2012", only_rsi_columns = any(is.rsi(x)), ...)
eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
eucast_exceptional_phenotypes(
x,
guideline = "EUCAST",
only_rsi_columns = any(is.rsi(x)),
...
)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
@ -57,6 +63,8 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_rsi_columns}{a logical to indicate whether only antibiotic columns must be detected that were \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand. Defaults to \code{TRUE} if any column of \code{x} is of class \verb{<rsi>}.}
\item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.}
\item{as_factor}{a \link{logical} to indicate whether the returned value should be an ordered \link{factor} (\code{TRUE}, default), or otherwise a \link{character} vector}
@ -174,7 +182,7 @@ This AMR package honours this new insight. Use \code{\link[=susceptibility]{susc
\section{Read more on Our Website!}{
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{