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