P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 19:01:51 +02:00
Code Releases Activity

(v0.8.0.9034) add cid to antivirals

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-11-23 12:39:57 +01:00
parent 267320f15f
commit e53cc4990c
37 changed files with 460 additions and 449 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
R/data.R
View File

@ -19,10 +19,11 @@
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Data set with ~450 antibiotics
#' Data sets with ~550 antimicrobials
#'
#' A data set containing all antibiotics. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this 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.
#' @format A \code{\link{data.frame}} with 453 observations and 13 variables:
#' Two data sets containing all antibiotics/antimycotics and antivirals. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from the \code{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.
#' @format
#' \strong{For the \code{antibiotics} data set: a \code{\link{data.frame}} with 452 observations and 13 variables:}
#' \describe{
#' \item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
@ -38,7 +39,20 @@
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' }
#' @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}
#'
#' \strong{For the \code{antivirals} data set: a \code{\link{data.frame}} with 102 observations and 9 variables:}
#' \describe{
#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
#' \item{\code{cid}}{Compound ID as found in PubChem}
#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
#' \item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
#' \item{\code{synonyms}}{Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' }
#' @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}.
#'
#' Synonyms (i.e. trade names) are derived from the Compound ID (\code{cid}) and consequently only available where a CID is available.
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
@ -48,26 +62,10 @@
#' European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{antivirals}} \code{\link{microorganisms}}
#' @seealso \code{\link{microorganisms}}
"antibiotics"
#' Data set with ~100 antivirals
#'
#' A data set containing all antivirals, according to the ATC code group 'J05' (Antivirals for systemic use).
#' @format A \code{\link{data.frame}} with 102 observations and 7 variables:
#' \describe{
#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC}
#' \item{\code{name}}{Official name as used by WHONET/EARS-Net or the WHO}
#' \item{\code{atc_group}}{Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC}
#' \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
#' \item{\code{oral_units}}{Units of \code{oral_ddd}}
#' \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
#' \item{\code{iv_units}}{Units of \code{iv_ddd}}
#' }
#' @source World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): \url{https://www.whocc.no/atc_ddd_index/}
#' @inheritSection WHOCC WHOCC
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{antibiotics}} \code{\link{microorganisms}}
#' @rdname antibiotics
"antivirals"
#' Data set with ~70,000 microorganisms