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(v0.8.0.9034) add cid to antivirals

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dr. M.S. (Matthijs) Berends
2019-11-23 12:39:57 +01:00
parent 267320f15f
commit e53cc4990c
37 changed files with 460 additions and 449 deletions
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26
man/antibiotics.Rd
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@@ -3,8 +3,9 @@
\docType{data}
\name{antibiotics}
\alias{antibiotics}
\title{Data set with ~450 antibiotics}
\format{A \code{\link{data.frame}} with 453 observations and 13 variables:
\alias{antivirals}
\title{Data sets with ~550 antimicrobials}
\format{\strong{For the \code{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 13 variables:}
\describe{
\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}
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
@@ -19,6 +20,19 @@
\item{\code{oral_units}}{Units of \code{oral_ddd}}
\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
\item{\code{iv_units}}{Units of \code{iv_ddd}}
}
\strong{For the \code{antivirals} data set: a \code{\link{data.frame}} with 102 observations and 9 variables:}
\describe{
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
\item{\code{cid}}{Compound ID as found in PubChem}
\item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
\item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
\item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
\item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
\item{\code{oral_units}}{Units of \code{oral_ddd}}
\item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
\item{\code{iv_units}}{Units of \code{iv_ddd}}
}}
\source{
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
@@ -29,12 +43,14 @@ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{htt
}
\usage{
antibiotics
antivirals
}
\description{
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.
Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from the \code{antibiotics} 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.
}
\details{
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}
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}.
Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and consequently only available where a CID is available.
}
@@ -56,6 +72,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\seealso{
\code{\link{antivirals}} \code{\link{microorganisms}}
\code{\link{microorganisms}}
}
\keyword{datasets}