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(v2.1.1.9226) update intrinsic_resistant, unit test fixes

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dr. M.S. (Matthijs) Berends
2025-03-27 15:20:22 +01:00
parent e6f88241b2
commit 969a42cc8c
29 changed files with 139318 additions and 244254 deletions
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6
man/antimicrobials.Rd
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@@ -8,14 +8,14 @@
\format{
\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
\itemize{
\item \code{ab}\cr antimcrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
\item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{\strong{This is a unique identifier.}}
\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 antimcrobial susceptibility testing (AST)
\item \code{abbr}\cr List of abbreviations as used in many countries, also for antimicrobial susceptibility testing (AST)
\item \code{synonyms}\cr Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs
\item \code{oral_units}\cr Units of \code{oral_ddd}
@@ -56,7 +56,7 @@ antimicrobials
antivirals
}
\description{
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 antimcrobial 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.
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}.