mirror of https://github.com/msberends/AMR.git
66 lines
2.2 KiB
R
Executable File
66 lines
2.2 KiB
R
Executable File
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/rsi.R
|
|
\name{as.rsi}
|
|
\alias{as.rsi}
|
|
\alias{is.rsi}
|
|
\alias{is.rsi.eligible}
|
|
\title{Class 'rsi'}
|
|
\usage{
|
|
as.rsi(x)
|
|
|
|
is.rsi(x)
|
|
|
|
is.rsi.eligible(x, threshold = 0.05)
|
|
}
|
|
\arguments{
|
|
\item{x}{vector}
|
|
|
|
\item{threshold}{maximum fraction of \code{x} that is allowed to fail transformation, see Examples}
|
|
}
|
|
\value{
|
|
Ordered factor with new class \code{rsi}
|
|
}
|
|
\description{
|
|
This transforms a vector 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{
|
|
The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains only valid antimicrobial interpretations (S and/or I and/or R), and \code{FALSE} otherwise.
|
|
}
|
|
\section{Read more on our website!}{
|
|
|
|
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
|
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
|
|
|
|
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(peni:rifa), 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`, threhold = 0.9) # succeeds
|
|
}
|
|
\seealso{
|
|
\code{\link{as.mic}}
|
|
}
|
|
\keyword{rsi}
|