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(v2.1.1.9267) update ATCs

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dr. M.S. (Matthijs) Berends
2025-05-01 11:48:49 +02:00
parent a455acdae3
commit 5e6bbdf3d1
24 changed files with 615 additions and 553 deletions
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10
man/antimicrobials.Rd
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@@ -29,7 +29,7 @@
\itemize{
\item \code{av}\cr Antiviral ID as used in this package (such as \code{ACI}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}} Combinations are codes that contain a \code{+} to indicate this, such as \code{ATA+COBI} for atazanavir/cobicistat.
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{\strong{This is a unique identifier.}}
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC
\item \code{atc}\cr ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, see \emph{Details}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
\item \code{atc_group}\cr Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
@@ -59,9 +59,13 @@ antivirals
Two data sets containing all antimicrobials 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{antimicrobials} data set. Three identifiers are included in this data set: an antimicrobial 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}.
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}. Do note that ATC codes are not unique. For example, J01CR02 is officially the ATC code for "amoxicillin and beta-lactamase inhibitor". Consequently, these two items from the \link{antimicrobials} data set both return \code{"J01CR02"}:
Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column \code{cid}) and consequently only available where a CID is available.
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ab_atc("amoxicillin/clavulanic acid")
ab_atc("amoxicillin/sulbactam")
}\if{html}{\out{</div>}}
Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column \code{cid}) and are consequently only available where a CID is available.
}
\section{Download Our Reference Data}{