mirror of https://github.com/msberends/AMR.git
60 lines
4.0 KiB
R
60 lines
4.0 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 ~450 antibiotics}
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\format{A \code{\link{data.frame}} with 454 observations and 13 variables:
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\describe{
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\item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
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\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
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\item{\code{cid}}{Compound ID as found in PubChem}
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\item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
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\item{\code{group}}{A short and concise group name, based on WHONET and WHOCC definitions}
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\item{\code{atc_group1}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}}
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\item{\code{atc_group2}}{Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}}
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\item{\code{abbr}}{List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)}
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\item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
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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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}}
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\source{
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World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
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WHONET 2019 software: \url{http://www.whonet.org/software.html}
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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. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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}
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\details{
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Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}
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Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and consequently only available where a CID is available.
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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 ~450 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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