AMR/man/as.rsi.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/rsi.R
\name{as.rsi}
\alias{as.rsi}
\alias{as.rsi.mic}
\alias{as.rsi.disk}
\alias{as.rsi.data.frame}
\alias{is.rsi}
\alias{is.rsi.eligible}
\title{Class 'rsi'}
\usage{
as.rsi(x, ...)

\method{as.rsi}{mic}(x, mo, ab, guideline = "EUCAST", ...)

\method{as.rsi}{disk}(x, mo, ab, guideline = "EUCAST", ...)

\method{as.rsi}{data.frame}(x, col_mo = NULL, guideline = "EUCAST",
  ...)

is.rsi(x)

is.rsi.eligible(x, threshold = 0.05)
}
\arguments{
\item{x}{vector of values (for class \code{mic}: an MIC value in mg/L, for class \code{disk}: a disk diffusion radius in millimeters)}

\item{...}{parameters passed on to methods}

\item{mo}{a microorganism code, generated with \code{\link{as.mo}}}

\item{ab}{an antibiotic code, generated with \code{\link{as.ab}}}

\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}

\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}

\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
}
\value{
Ordered factor with new class \code{rsi}
}
\description{
Interpret MIC values according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
}
\details{
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.

After using \code{as.rsi}, you can use \code{\link{eucast_rules}} to (1) apply inferred susceptibility and resistance based on results of other antibiotics and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.

The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter.
}
\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}

\examples{
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
is.rsi(rsi_data)

# this can also coerce combined MIC/RSI values:
as.rsi("<= 0.002; S") # will return S

# interpret MIC values
as.rsi(x = as.mic(2),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")
as.rsi(x = as.mic(4),
       mo = as.mo("S. pneumoniae"),
       ab = "AMX",
       guideline = "EUCAST")

plot(rsi_data)    # for percentages
barplot(rsi_data) # for frequencies
freq(rsi_data)    # frequency table with informative header

# using dplyr's mutate
library(dplyr)
septic_patients \%>\%
  mutate_at(vars(PEN:RIF), as.rsi)


# fastest way to transform all columns with already valid AB results to class `rsi`:
septic_patients \%>\%
  mutate_if(is.rsi.eligible,
            as.rsi)

# default threshold of `is.rsi.eligible` is 5\%.
is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid
is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
}
\seealso{
\code{\link{as.mic}}
}
\keyword{rsi}