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(v1.5.0.9016) only_rsi_columns update, documentation

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dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
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33
man/antibiotic_class_selectors.Rd
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@@ -14,42 +14,45 @@
\alias{fluoroquinolones}
\alias{glycopeptides}
\alias{macrolides}
\alias{oxazolidinones}
\alias{penicillins}
\alias{tetracyclines}
\title{Antibiotic Class Selectors}
\usage{
ab_class(ab_class, only_rsi_columns = NULL)
ab_class(ab_class, only_rsi_columns = FALSE)
aminoglycosides(only_rsi_columns = NULL)
aminoglycosides(only_rsi_columns = FALSE)
carbapenems(only_rsi_columns = NULL)
carbapenems(only_rsi_columns = FALSE)
cephalosporins(only_rsi_columns = NULL)
cephalosporins(only_rsi_columns = FALSE)
cephalosporins_1st(only_rsi_columns = NULL)
cephalosporins_1st(only_rsi_columns = FALSE)
cephalosporins_2nd(only_rsi_columns = NULL)
cephalosporins_2nd(only_rsi_columns = FALSE)
cephalosporins_3rd(only_rsi_columns = NULL)
cephalosporins_3rd(only_rsi_columns = FALSE)
cephalosporins_4th(only_rsi_columns = NULL)
cephalosporins_4th(only_rsi_columns = FALSE)
cephalosporins_5th(only_rsi_columns = NULL)
cephalosporins_5th(only_rsi_columns = FALSE)
fluoroquinolones(only_rsi_columns = NULL)
fluoroquinolones(only_rsi_columns = FALSE)
glycopeptides(only_rsi_columns = NULL)
glycopeptides(only_rsi_columns = FALSE)
macrolides(only_rsi_columns = NULL)
macrolides(only_rsi_columns = FALSE)
penicillins(only_rsi_columns = NULL)
oxazolidinones(only_rsi_columns = FALSE)
tetracyclines(only_rsi_columns = NULL)
penicillins(only_rsi_columns = FALSE)
tetracyclines(only_rsi_columns = FALSE)
}
\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.}
\item{only_rsi_columns}{a logical to indicate whether only columns of class \href{[rsi]}{\verb{<rsi>}} must be selected (defaults to \code{FALSE})}
}
\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, "."), "")}}