mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:06:12 +01:00
58 lines
1.6 KiB
R
Executable File
58 lines
1.6 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/mic.R
|
|
\name{as.mic}
|
|
\alias{as.mic}
|
|
\alias{is.mic}
|
|
\title{Class 'mic'}
|
|
\usage{
|
|
as.mic(x, na.rm = FALSE)
|
|
|
|
is.mic(x)
|
|
}
|
|
\arguments{
|
|
\item{x}{vector}
|
|
|
|
\item{na.rm}{a logical indicating whether missing values should be removed}
|
|
}
|
|
\value{
|
|
Ordered factor with new class \code{mic}
|
|
}
|
|
\description{
|
|
This transforms a vector to a new class \code{mic}, which is an ordered factor with valid MIC values as levels. Invalid MIC values will be translated as \code{NA} with a warning.
|
|
}
|
|
\details{
|
|
Interpret MIC values as RSI values with \code{\link{as.rsi}}. It supports guidelines from EUCAST and CLSI.
|
|
}
|
|
\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 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{
|
|
mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16"))
|
|
is.mic(mic_data)
|
|
|
|
# this can also coerce combined MIC/RSI values:
|
|
as.mic("<=0.002; S") # will return <=0.002
|
|
|
|
# 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(mic_data)
|
|
barplot(mic_data)
|
|
|
|
library(clean)
|
|
freq(mic_data)
|
|
}
|
|
\seealso{
|
|
\code{\link{as.rsi}}
|
|
}
|
|
\keyword{mic}
|