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indicate unique identifiers

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dr. M.S. (Matthijs) Berends
2023-07-12 21:26:32 +02:00
parent ea2a4652e9
commit eff164ecb1
8 changed files with 31 additions and 24 deletions
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12
man/antibiotics.Rd
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@@ -8,9 +8,9 @@
\format{
\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 483 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{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{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. \emph{This is a unique identifier.}
\item \code{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.}
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{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"}
@@ -27,10 +27,10 @@
\subsection{For the \link{antivirals} data set: a \link[tibble:tibble]{tibble} with 120 observations and 11 variables:}{
\itemize{
\item \code{av}\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{name}\cr Official name as used by WHONET/EARS-Net or the WHO
\item \code{av}\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. \emph{This is a unique identifier.}
\item \code{name}\cr Official name as used by WHONET/EARS-Net or the WHO. \emph{This is a unique identifier.}
\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{cid}\cr Compound ID as found in PubChem. \emph{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
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment

2
man/clinical_breakpoints.Rd
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@@ -42,7 +42,7 @@ Clinical breakpoints in this package were validated through and imported from \h
\subsection{Response from CLSI and EUCAST}{
The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the \code{AMR} package.
The CEO of CLSI and the chairman of EUCAST have endorsed the work and public use of this \code{AMR} package (and consequently the use of their breakpoints) in June 2023, when future development of distributing clinical breakpoints was discussed in a meeting between CLSI, EUCAST, the WHO, and developers of WHONET and the \code{AMR} package.
}
\subsection{Download}{

4
man/microorganisms.Rd
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@@ -7,8 +7,8 @@
\format{
A \link[tibble:tibble]{tibble} with 52 169 observations and 23 variables:
\itemize{
\item \code{mo}\cr ID of microorganism as used by this package
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.
\item \code{mo}\cr ID of microorganism as used by this package. \emph{This is a unique identifier.}
\item \code{fullname}\cr Full name, like \code{"Escherichia coli"}. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon. \emph{This is a unique identifier.}
\item \code{status} \cr Status of the taxon, either "accepted" or "synonym"
\item \code{kingdom}, \code{phylum}, \code{class}, \code{order}, \code{family}, \code{genus}, \code{species}, \code{subspecies}\cr Taxonomic rank of the microorganism
\item \code{rank}\cr Text of the taxonomic rank of the microorganism, such as \code{"species"} or \code{"genus"}

2
man/microorganisms.codes.Rd
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@@ -7,7 +7,7 @@
\format{
A \link[tibble:tibble]{tibble} with 4 957 observations and 2 variables:
\itemize{
\item \code{code}\cr Commonly used code of a microorganism
\item \code{code}\cr Commonly used code of a microorganism. \emph{This is a unique identifier.}
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set
}
}