mirror of https://github.com/msberends/AMR.git
55 lines
1.6 KiB
Plaintext
55 lines
1.6 KiB
Plaintext
|
% Generated by roxygen2: do not edit by hand
|
||
|
|
% Please edit documentation in R/rsi_analysis.R
|
||
|
|
\name{rsi}
|
||
|
|
\alias{rsi}
|
||
|
|
\title{Resistance of isolates}
|
||
|
|
\usage{
|
||
|
|
rsi(ab1, ab2 = NA, interpretation = "IR", minimum = 30, percent = FALSE,
|
||
|
|
info = FALSE, warning = FALSE)
|
||
|
|
}
|
||
|
|
\arguments{
|
||
|
|
\item{ab1, ab2}{list with interpretations of an antibiotic}
|
||
|
|
|
||
|
|
\item{interpretation}{antimicrobial interpretation of which the portion must be calculated. Valid values are \code{"S"}, \code{"SI"}, \code{"I"}, \code{"IR"} or \code{"R"}.}
|
||
|
|
|
||
|
|
\item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA} with a warning (when \code{warning = TRUE}).}
|
||
|
|
|
||
|
|
\item{percent}{return output as percent (text), will else (at default) be a double}
|
||
|
|
|
||
|
|
\item{info}{calculate the amount of available isolates and print it, like \code{n = 423}}
|
||
|
|
|
||
|
|
\item{warning}{show a warning when the available amount of isolates is below \code{minimum}}
|
||
|
|
}
|
||
|
|
\value{
|
||
|
|
Double or, when \code{percent = TRUE}, a character.
|
||
|
|
}
|
||
|
|
\description{
|
||
|
|
This function can be used in \code{\link[dplyr]{summarise}}, see \emph{Examples}. CaBerekent het percentage S, SI, I, IR of R van een lijst isolaten.
|
||
|
|
}
|
||
|
|
\details{
|
||
|
|
This function uses the \code{\link{rsi_df}} function internally.
|
||
|
|
}
|
||
|
|
\examples{
|
||
|
|
\dontrun{
|
||
|
|
tbl \%>\%
|
||
|
|
group_by(year, hospital) \%>\%
|
||
|
|
summarise(
|
||
|
|
isolates = n(),
|
||
|
|
cipro = rsi(cipr, percent = TRUE),
|
||
|
|
amoxi = rsi(amox, percent = TRUE)
|
||
|
|
)
|
||
|
|
|
||
|
|
tbl \%>\%
|
||
|
|
group_by(hospital) \%>\%
|
||
|
|
summarise(cipr = rsi(cipr))
|
||
|
|
|
||
|
|
rsi(isolates$amox)
|
||
|
|
|
||
|
|
rsi(isolates$amcl, interpretation = "S")
|
||
|
|
}
|
||
|
|
}
|
||
|
|
\keyword{antibiotics}
|
||
|
|
\keyword{isolate}
|
||
|
|
\keyword{isolates}
|
||
|
|
\keyword{rsi}
|