% Generated by roxygen2: do not edit by hand % Please edit documentation in R/rsi_IR.R \name{rsi_IR} \alias{rsi_IR} \alias{rsi_R} \alias{rsi_I} \alias{rsi_SI} \alias{rsi_S} \alias{resistance} \alias{intermediate} \alias{susceptibility} \alias{rsi_n} \alias{n_rsi} \title{Calculate resistance of isolates} \source{ \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. } \usage{ rsi_R(ab1, minimum = 30, as_percent = FALSE) rsi_IR(ab1, minimum = 30, as_percent = FALSE) rsi_I(ab1, minimum = 30, as_percent = FALSE) rsi_SI(ab1, ab2 = NULL, minimum = 30, as_percent = FALSE) rsi_S(ab1, ab2 = NULL, minimum = 30, as_percent = FALSE) resistance(ab1, include_I = TRUE, minimum = 30, as_percent = FALSE) intermediate(ab1, minimum = 30, as_percent = FALSE) susceptibility(ab1, ab2 = NULL, include_I = FALSE, minimum = 30, as_percent = FALSE) rsi_n(ab1, ab2 = NULL) n_rsi(ab1, ab2 = NULL) } \arguments{ \item{ab1}{vector of antibiotic interpretations, they will be transformed internally with \code{\link{as.rsi}}} \item{minimum}{minimal amount of available isolates. Any number lower than \code{minimum} will return \code{NA}. The default number of \code{30} isolates is advised by the CLSI as best practice, see Source.} \item{as_percent}{logical to indicate whether the output must be returned as percent (text), will else be a double} \item{ab2}{like \code{ab}, a vector of antibiotic interpretations. Use this to calculate (the lack of) co-resistance: the probability where one of two drugs have a susceptible result. See Examples.} \item{include_I}{logical to indicate whether antimicrobial interpretations of "I" should be included} } \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}. \cr\cr \code{rsi_R} and \code{rsi_IR} can be used to calculate resistance, \code{rsi_S} and \code{rsi_SI} can be used to calculate susceptibility.\cr \code{rsi_n} counts all cases where antimicrobial interpretations are available. } \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. The functions \code{resistance} and \code{susceptibility} are wrappers around \code{rsi_IR} and \code{rsi_S}, respectively. All functions use hybrid evaluation (i.e. using C++), which makes these functions 20-30 times faster than the old \code{\link{rsi}} function. This latter function is still available for backwards compatibility but is deprecated. \if{html}{ \cr\cr To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula: \out{