mirror of https://github.com/msberends/AMR.git
61 lines
3.9 KiB
R
61 lines
3.9 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{antibiotics}
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\alias{antibiotics}
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\title{Data set with ~500 antibiotics}
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\format{A \code{\link{data.frame}} with 488 observations and 17 variables:
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\describe{
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\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical), like \code{J01CR02}}
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\item{\code{ears_net}}{EARS-Net code (European Antimicrobial Resistance Surveillance Network), like \code{AMC}}
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\item{\code{certe}}{Certe code, like \code{amcl}}
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\item{\code{umcg}}{UMCG code, like \code{AMCL}}
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\item{\code{abbr}}{Abbreviation as used by many countries, used internally by \code{\link{as.atc}}}
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\item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and beta-lactamase inhibitor"}}
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\item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
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\item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
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\item{\code{trade_name}}{Trade name as used by many countries (a total of 294), used internally by \code{\link{as.atc}}}
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\item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
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\item{\code{oral_units}}{Units of \code{ddd_units}}
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\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
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\item{\code{iv_units}}{Units of \code{iv_ddd}}
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\item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
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\item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
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\item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
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\item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
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}}
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\source{
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World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
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Table antibiotic coding EARSS (from WHONET 5.3): \url{http://www.madsonline.dk/Tutorials/landskoder_antibiotika_WM.pdf}
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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}
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European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
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}
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\usage{
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antibiotics
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}
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\description{
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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.
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}
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\section{WHOCC}{
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\if{html}{\figure{logo_who.png}{options: height=60px style=margin-bottom:5px} \cr}
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This package contains \strong{all ~500 antimicrobial drugs} and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, \url{https://www.whocc.no}) and the Pharmaceuticals Community Register of the European Commission (\url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}).
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These have become the gold standard for international drug utilisation monitoring and research.
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The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.
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}
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\section{Read more on our website!}{
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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}.
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}
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\seealso{
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\code{\link{microorganisms}}
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}
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\keyword{datasets}
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