mirror of https://github.com/msberends/AMR.git
56 lines
1.7 KiB
R
Executable File
56 lines
1.7 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mic.R
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\name{as.mic}
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\alias{as.mic}
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\alias{MIC}
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\alias{is.mic}
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\title{Class 'mic'}
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\usage{
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as.mic(x, na.rm = FALSE)
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is.mic(x)
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}
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\arguments{
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\item{x}{vector}
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\item{na.rm}{a logical indicating whether missing values should be removed}
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}
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\value{
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Ordered \code{\link{factor}} with new class \code{\link{mic}}
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}
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\description{
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This transforms a vector to a new class \code{\link{mic}}, which is an ordered \code{\link{factor}} with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
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}
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\details{
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To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST and CLSI.
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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 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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mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
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is.mic(mic_data)
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# this can also coerce combined MIC/RSI values:
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as.mic("<=0.002; S") # will return <=0.002
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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(mic_data)
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barplot(mic_data)
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freq(mic_data)
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}
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\seealso{
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\code{\link[=as.rsi]{as.rsi()}}
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}
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