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(v1.4.0.9050) ab selectors base R

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dr. M.S. (Matthijs) Berends
2020-12-27 20:32:40 +01:00
parent 175e33abba
commit afc325c314
33 changed files with 88 additions and 65 deletions
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man/mdro.Rd
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@ -40,7 +40,7 @@ mdr_cmi2012(x, guideline = "CMI2012", ...)
eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
}
\arguments{
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be omitted when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
\item{x}{a \link{data.frame} with antibiotics columns, like \code{AMX} or \code{amox}. Can be left blank when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.}
\item{guideline}{a specific guideline to follow. When left empty, the publication by Magiorakos \emph{et al.} (2012, Clinical Microbiology and Infection) will be followed, please see \emph{Details}.}
@ -72,7 +72,7 @@ Ordered \link{factor} with levels \code{Negative} < \verb{Positive, unconfirmed}
Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.
}
\details{
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be omitted, please see \emph{Examples}.
These functions are context-aware when used inside \code{dplyr} verbs, such as \code{filter()}, \code{mutate()} and \code{summarise()}. This means that then the \code{x} argument can be left blank, please see \emph{Examples}.
For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}).