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99 lines
3.7 KiB
R
Executable File
99 lines
3.7 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/rsi.R
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\name{as.rsi}
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\alias{as.rsi}
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\alias{as.rsi.mic}
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\alias{as.rsi.disk}
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\alias{as.rsi.data.frame}
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\alias{is.rsi}
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\alias{is.rsi.eligible}
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\title{Class 'rsi'}
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\usage{
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as.rsi(x, ...)
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\method{as.rsi}{mic}(x, mo, ab, guideline = "EUCAST", ...)
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\method{as.rsi}{disk}(x, mo, ab, guideline = "EUCAST", ...)
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\method{as.rsi}{data.frame}(x, col_mo = NULL, guideline = "EUCAST",
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...)
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is.rsi(x)
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is.rsi.eligible(x, threshold = 0.05)
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}
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\arguments{
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\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)}
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\item{...}{parameters passed on to methods}
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\item{mo}{a microorganism code, generated with \code{\link{as.mo}}}
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\item{ab}{an antibiotic code, generated with \code{\link{as.ab}}}
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\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
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\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
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\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
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}
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\value{
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Ordered factor with new class \code{rsi}
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}
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\description{
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Interpret MIC values according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class \code{rsi}, which is an ordered factor with levels \code{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
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}
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\details{
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Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.
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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.
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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.
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}
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\section{Read more on our website!}{
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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}.
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}
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\examples{
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rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370)))
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rsi_data <- as.rsi(c(rep("S", 474), rep("I", 36), rep("R", 370), "A", "B", "C"))
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is.rsi(rsi_data)
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# this can also coerce combined MIC/RSI values:
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as.rsi("<= 0.002; S") # will return S
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# interpret MIC values
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as.rsi(x = as.mic(2),
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mo = as.mo("S. pneumoniae"),
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ab = "AMX",
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guideline = "EUCAST")
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as.rsi(x = as.mic(4),
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mo = as.mo("S. pneumoniae"),
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ab = "AMX",
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guideline = "EUCAST")
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plot(rsi_data) # for percentages
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barplot(rsi_data) # for frequencies
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freq(rsi_data) # frequency table with informative header
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# using dplyr's mutate
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library(dplyr)
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septic_patients \%>\%
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mutate_at(vars(PEN:RIF), as.rsi)
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# fastest way to transform all columns with already valid AB results to class `rsi`:
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septic_patients \%>\%
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mutate_if(is.rsi.eligible,
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as.rsi)
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# default threshold of `is.rsi.eligible` is 5\%.
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is.rsi.eligible(WHONET$`First name`) # fails, >80\% is invalid
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is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds
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}
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\seealso{
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\code{\link{as.mic}}
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}
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\keyword{rsi}
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