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mirror of https://github.com/msberends/AMR.git synced 2025-07-12 20:21:58 +02:00

(v1.5.0.9014) only_rsi_columns, is.rsi.eligible improvement

This commit is contained in:
2021-02-02 23:57:35 +01:00
parent 20d638c193
commit 2eca8c3f01
246 changed files with 1171 additions and 965 deletions

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@ -18,36 +18,38 @@
\alias{tetracyclines}
\title{Antibiotic Class Selectors}
\usage{
ab_class(ab_class)
ab_class(ab_class, only_rsi_columns = NULL)
aminoglycosides()
aminoglycosides(only_rsi_columns = NULL)
carbapenems()
carbapenems(only_rsi_columns = NULL)
cephalosporins()
cephalosporins(only_rsi_columns = NULL)
cephalosporins_1st()
cephalosporins_1st(only_rsi_columns = NULL)
cephalosporins_2nd()
cephalosporins_2nd(only_rsi_columns = NULL)
cephalosporins_3rd()
cephalosporins_3rd(only_rsi_columns = NULL)
cephalosporins_4th()
cephalosporins_4th(only_rsi_columns = NULL)
cephalosporins_5th()
cephalosporins_5th(only_rsi_columns = NULL)
fluoroquinolones()
fluoroquinolones(only_rsi_columns = NULL)
glycopeptides()
glycopeptides(only_rsi_columns = NULL)
macrolides()
macrolides(only_rsi_columns = NULL)
penicillins()
penicillins(only_rsi_columns = NULL)
tetracyclines()
tetracyclines(only_rsi_columns = NULL)
}
\arguments{
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{<rsi>}} must be selected. If set to \code{NULL} (default), it will be \code{TRUE} if any column of the data was \href{[rsi]}{transformed to class \verb{<rsi>}} on beforehand, and \code{FALSE} otherwise.}
}
\description{
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
@ -72,7 +74,7 @@ All reference data sets (about microorganisms, antibiotics, R/SI interpretation,
\section{Read more on Our Website!}{
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
On our website \url{https://msberends.github.io/AMR/} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR data analysis, the \href{https://msberends.github.io/AMR/reference/}{complete documentation of all functions} and \href{https://msberends.github.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. As we would like to better understand the backgrounds and needs of our users, please \href{https://msberends.github.io/AMR/survey.html}{participate in our survey}!
}
\examples{