mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
117 lines
4.3 KiB
R
117 lines
4.3 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/ab_property.R
|
|
\name{ab_property}
|
|
\alias{ab_property}
|
|
\alias{ab_name}
|
|
\alias{ab_atc}
|
|
\alias{ATC}
|
|
\alias{ab_cid}
|
|
\alias{ab_synonyms}
|
|
\alias{ab_tradenames}
|
|
\alias{ab_group}
|
|
\alias{ab_atc_group1}
|
|
\alias{ab_atc_group2}
|
|
\alias{ab_ddd}
|
|
\alias{ab_info}
|
|
\title{Property of an antibiotic}
|
|
\usage{
|
|
ab_name(x, language = get_locale(), tolower = FALSE, ...)
|
|
|
|
ab_atc(x, ...)
|
|
|
|
ab_cid(x, ...)
|
|
|
|
ab_synonyms(x, ...)
|
|
|
|
ab_tradenames(x, ...)
|
|
|
|
ab_group(x, language = get_locale(), ...)
|
|
|
|
ab_atc_group1(x, language = get_locale(), ...)
|
|
|
|
ab_atc_group2(x, language = get_locale(), ...)
|
|
|
|
ab_ddd(x, administration = "oral", units = FALSE, ...)
|
|
|
|
ab_info(x, language = get_locale(), ...)
|
|
|
|
ab_property(x, property = "name", language = get_locale(), ...)
|
|
}
|
|
\arguments{
|
|
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.ab]{as.ab()}}}
|
|
|
|
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
|
|
|
\item{tolower}{logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
|
|
|
|
\item{...}{other parameters passed on to \code{\link[=as.ab]{as.ab()}}}
|
|
|
|
\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
|
|
|
|
\item{units}{a logical to indicate whether the units instead of the DDDs itself must be returned, see Examples}
|
|
|
|
\item{property}{one of the column names of one of the \link{antibiotics} data set}
|
|
}
|
|
\value{
|
|
\itemize{
|
|
\item An \code{\link{integer}} in case of \code{\link[=ab_cid]{ab_cid()}}
|
|
\item A named \code{\link{list}} in case of \code{\link[=ab_info]{ab_info()}} and multiple \code{\link[=ab_synonyms]{ab_synonyms()}}/\code{\link[=ab_tradenames]{ab_tradenames()}}
|
|
\item A \code{\link{double}} in case of \code{\link[=ab_ddd]{ab_ddd()}}
|
|
\item A \code{\link{character}} in all other cases
|
|
}
|
|
}
|
|
\description{
|
|
Use these functions to return a specific property of an antibiotic from the \link{antibiotics} data set. All input values will be evaluated internally with \code{\link[=as.ab]{as.ab()}}.
|
|
}
|
|
\details{
|
|
All output will be \link{translate}d where possible.
|
|
}
|
|
\section{Source}{
|
|
|
|
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
|
|
|
|
WHONET 2019 software: \url{http://www.whonet.org/software.html}
|
|
|
|
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{http://ec.europa.eu/health/documents/community-register/html/atc.htm}
|
|
}
|
|
|
|
\section{Read more on our website!}{
|
|
|
|
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
|
|
}
|
|
|
|
\examples{
|
|
# all properties:
|
|
ab_name("AMX") # "Amoxicillin"
|
|
ab_atc("AMX") # J01CA04 (ATC code from the WHO)
|
|
ab_cid("AMX") # 33613 (Compound ID from PubChem)
|
|
|
|
ab_synonyms("AMX") # a list with brand names of amoxicillin
|
|
ab_tradenames("AMX") # same
|
|
|
|
ab_group("AMX") # "Beta-lactams/penicillins"
|
|
ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
|
|
ab_atc_group2("AMX") # "Penicillins with extended spectrum"
|
|
|
|
ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
|
|
ab_name(x = c("AMC", "PLB"),
|
|
tolower = TRUE) # "amoxicillin/clavulanic acid" "polymyxin B"
|
|
|
|
ab_ddd("AMX", "oral") # 1
|
|
ab_ddd("AMX", "oral", units = TRUE) # "g"
|
|
ab_ddd("AMX", "iv") # 1
|
|
ab_ddd("AMX", "iv", units = TRUE) # "g"
|
|
|
|
ab_info("AMX") # all properties as a list
|
|
|
|
# all ab_* functions use as.ab() internally:
|
|
ab_name("Fluclox") # "Flucloxacillin"
|
|
ab_name("fluklox") # "Flucloxacillin"
|
|
ab_name("floxapen") # "Flucloxacillin"
|
|
ab_name(21319) # "Flucloxacillin" (using CID)
|
|
ab_name("J01CF05") # "Flucloxacillin" (using ATC)
|
|
}
|
|
\seealso{
|
|
\link{antibiotics}
|
|
}
|