mirror of https://github.com/msberends/AMR.git
52 lines
3.1 KiB
R
52 lines
3.1 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/data.R
|
|
\docType{data}
|
|
\name{antibiotics}
|
|
\alias{antibiotics}
|
|
\title{Data set with ~500 antibiotics}
|
|
\format{A \code{\link{data.frame}} with 488 observations and 17 variables:
|
|
\describe{
|
|
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical), like \code{J01CR02}}
|
|
\item{\code{ears_net}}{EARS-Net code (European Antimicrobial Resistance Surveillance Network), like \code{AMC}}
|
|
\item{\code{certe}}{Certe code, like \code{amcl}}
|
|
\item{\code{umcg}}{UMCG code, like \code{AMCL}}
|
|
\item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
|
|
\item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and beta-lactamase inhibitor"}}
|
|
\item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
|
|
\item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
|
|
\item{\code{trade_name}}{Trade name as used by many countries (a total of 294), used internally by \code{\link{as.atc}}}
|
|
\item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
|
|
\item{\code{oral_units}}{Units of \code{ddd_units}}
|
|
\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
|
|
\item{\code{iv_units}}{Units of \code{iv_ddd}}
|
|
\item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
|
|
\item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
|
|
\item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
|
|
\item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
|
|
}}
|
|
\source{
|
|
- World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
|
|
|
|
Table antibiotic coding EARSS (from WHONET 5.3): \url{http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf}
|
|
|
|
EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016: \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
|
|
|
|
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
|
|
}
|
|
\usage{
|
|
antibiotics
|
|
}
|
|
\description{
|
|
A data set containing all antibiotics with a J0 code and some other antimicrobial agents, with their DDDs. Except for trade names and abbreviations, all properties were downloaded from the WHO, see Source.
|
|
}
|
|
\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 omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
|
|
}
|
|
|
|
\seealso{
|
|
\code{\link{microorganisms}}
|
|
}
|
|
\keyword{datasets}
|