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(v1.7.1.9023) Removed filter_ functions, new set_ab_names(), ATC code update, ab selector update, fixes #46 and fixed #47

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dr. M.S. (Matthijs) Berends
2021-08-16 21:54:34 +02:00
parent 4e1efd902c
commit a2d249962f
248 changed files with 2377 additions and 12201 deletions
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6
man/antibiotics.Rd
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@@ -9,10 +9,10 @@
\subsection{For the \link{antibiotics} data set: a \link{data.frame} with 456 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
\item \code{cid}\cr Compound ID as found in PubChem
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
\item \code{group}\cr A short and concise group name, based on WHONET and WHOCC definitions
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}
\item \code{atc_group1}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like \code{"Macrolides, lincosamides and streptogramins"}
\item \code{atc_group2}\cr Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like \code{"Macrolides"}
\item \code{abbr}\cr List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
@@ -27,7 +27,7 @@
\subsection{For the \link{antivirals} data set: a \link{data.frame} with 102 observations and 9 variables:}{
\itemize{
\item \code{atc}\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
\item \code{cid}\cr Compound ID as found in PubChem
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO
\item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
@@ -54,7 +54,7 @@ antibiotics
antivirals
}
\description{
Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{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.
Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{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. Note that some drugs have multiple ATC 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}.