P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-13 01:51:52 +02:00
Code Releases Activity

(v2.1.1.9064) update all microbial taxonomy, add mycobank, big documentation update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-07-16 14:51:57 +02:00
parent 4f9db23684
commit 640888f408
191 changed files with 321091 additions and 89382 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
man/antibiotics.Rd
View File

@ -8,9 +8,9 @@
\format{
\subsection{For the \link{antibiotics} data set: a \link[tibble:tibble]{tibble} with 485 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. \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{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{\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"}
@ -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 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{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{This is a unique identifier.}
\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{cid}\cr Compound ID as found in PubChem. \emph{This is a unique identifier.}
\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
\item \code{oral_ddd}\cr Defined Daily Dose (DDD), oral treatment