P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 06:01:53 +02:00
Code Releases Activity

Replace RSI with SIR

Browse Source
This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
Download Patch File Download Diff File Expand all files Collapse all files

64
man/antibiotic_class_selectors.Rd
View File

@ -34,66 +34,66 @@
\alias{not_intrinsic_resistant}
\title{Antibiotic Selectors}
\usage{
ab_class(ab_class, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
ab_class(ab_class, only_sir_columns = FALSE, only_treatable = TRUE, ...)
ab_selector(filter, only_rsi_columns = FALSE, only_treatable = TRUE, ...)
ab_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE, ...)
aminoglycosides(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE, ...)
aminopenicillins(only_rsi_columns = FALSE, ...)
aminopenicillins(only_sir_columns = FALSE, ...)
antifungals(only_rsi_columns = FALSE, ...)
antifungals(only_sir_columns = FALSE, ...)
antimycobacterials(only_rsi_columns = FALSE, ...)
antimycobacterials(only_sir_columns = FALSE, ...)
betalactams(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)
carbapenems(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)
cephalosporins(only_rsi_columns = FALSE, ...)
cephalosporins(only_sir_columns = FALSE, ...)
cephalosporins_1st(only_rsi_columns = FALSE, ...)
cephalosporins_1st(only_sir_columns = FALSE, ...)
cephalosporins_2nd(only_rsi_columns = FALSE, ...)
cephalosporins_2nd(only_sir_columns = FALSE, ...)
cephalosporins_3rd(only_rsi_columns = FALSE, ...)
cephalosporins_3rd(only_sir_columns = FALSE, ...)
cephalosporins_4th(only_rsi_columns = FALSE, ...)
cephalosporins_4th(only_sir_columns = FALSE, ...)
cephalosporins_5th(only_rsi_columns = FALSE, ...)
cephalosporins_5th(only_sir_columns = FALSE, ...)
fluoroquinolones(only_rsi_columns = FALSE, ...)
fluoroquinolones(only_sir_columns = FALSE, ...)
glycopeptides(only_rsi_columns = FALSE, ...)
glycopeptides(only_sir_columns = FALSE, ...)
lincosamides(only_rsi_columns = FALSE, ...)
lincosamides(only_sir_columns = FALSE, ...)
lipoglycopeptides(only_rsi_columns = FALSE, ...)
lipoglycopeptides(only_sir_columns = FALSE, ...)
macrolides(only_rsi_columns = FALSE, ...)
macrolides(only_sir_columns = FALSE, ...)
oxazolidinones(only_rsi_columns = FALSE, ...)
oxazolidinones(only_sir_columns = FALSE, ...)
penicillins(only_rsi_columns = FALSE, ...)
penicillins(only_sir_columns = FALSE, ...)
polymyxins(only_rsi_columns = FALSE, only_treatable = TRUE, ...)
polymyxins(only_sir_columns = FALSE, only_treatable = TRUE, ...)
streptogramins(only_rsi_columns = FALSE, ...)
streptogramins(only_sir_columns = FALSE, ...)
quinolones(only_rsi_columns = FALSE, ...)
quinolones(only_sir_columns = FALSE, ...)
tetracyclines(only_rsi_columns = FALSE, ...)
tetracyclines(only_sir_columns = FALSE, ...)
trimethoprims(only_rsi_columns = FALSE, ...)
trimethoprims(only_sir_columns = FALSE, ...)
ureidopenicillins(only_rsi_columns = FALSE, ...)
ureidopenicillins(only_sir_columns = FALSE, ...)
administrable_per_os(only_rsi_columns = FALSE, ...)
administrable_per_os(only_sir_columns = FALSE, ...)
administrable_iv(only_rsi_columns = FALSE, ...)
administrable_iv(only_sir_columns = FALSE, ...)
not_intrinsic_resistant(
only_rsi_columns = FALSE,
only_sir_columns = FALSE,
col_mo = NULL,
version_expertrules = 3.3,
...
@ -102,7 +102,7 @@ not_intrinsic_resistant(
\arguments{
\item{ab_class}{an antimicrobial class or a part of it, such as \code{"carba"} and \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 \link{logical} to indicate whether only columns of class \code{rsi} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
\item{only_sir_columns}{a \link{logical} to indicate whether only columns of class \code{sir} must be selected (defaults to \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}}
\item{only_treatable}{a \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
@ -166,7 +166,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
\section{Reference Data Publicly Available}{
All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}
\examples{