% Generated by roxygen2: do not edit by hand % Please edit documentation in R/resistance.R \name{resistance} \alias{resistance} \alias{susceptibility} \alias{n_rsi} \alias{rsi} \title{Calculate resistance of isolates} \usage{ resistance(ab, include_I = TRUE, minimum = 30, as_percent = FALSE) susceptibility(ab1, ab2 = NULL, include_I = FALSE, minimum = 30, as_percent = FALSE) n_rsi(ab1, ab2 = NULL) rsi(ab1, ab2 = NULL, interpretation = "IR", minimum = 30, as_percent = FALSE) } \arguments{ \item{ab, ab1, ab2}{vector of antibiotic interpretations, they will be transformed internally with \code{\link{as.rsi}}} \item{include_I}{logical to indicate whether antimicrobial interpretations of "I" should be included} \item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA}.} \item{as_percent}{logical to indicate whether the output must be returned as percent (text), will else be a double} \item{interpretation}{antimicrobial interpretation} } \value{ Double or, when \code{as_percent = TRUE}, a character. } \description{ These functions can be used to calculate the (co-)resistance of microbial isolates (i.e. percentage S, SI, I, IR or R). All functions can be used in \code{dplyr}s \code{\link[dplyr]{summarise}} and support grouped variables, see \emph{Examples}. } \details{ \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set. All return values are calculated using hybrid evaluation (i.e. using C++), which makes these functions 60-65 times faster than in \code{AMR} v0.2.0 and below. The \code{rsi} function is available for backwards compatibility and deprecated. It now uses the \code{resistance} and \code{susceptibility} functions internally, based on the \code{interpretation} parameter. \if{html}{ \cr To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula: \out{