% 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{dplyr}s \code{\link[dplyr]{summarise}}, see \emph{Examples}. Calculate the percentage S, SI, I, IR or R of a vector of isolates. } \details{ This function uses the \code{\link{rsi_df}} function internally. } \examples{ \dontrun{ tbl \%>\% group_by(hospital) \%>\% summarise(cipr = rsi(cipr)) tbl \%>\% group_by(year, hospital) \%>\% summarise( isolates = n(), cipro = rsi(cipr \%>\% as.rsi(), percent = TRUE), amoxi = rsi(amox \%>\% as.rsi(), percent = TRUE)) rsi(as.rsi(isolates$amox)) rsi(as.rsi(isolates$amcl), interpretation = "S") } } \keyword{antibiotics} \keyword{isolate} \keyword{isolates} \keyword{rsi}