mirror of https://github.com/msberends/AMR.git
178 lines
6.4 KiB
R
178 lines
6.4 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_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}
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\alias{ATC}
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\alias{ab_atc_group1}
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\alias{ab_atc_group2}
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\alias{ab_loinc}
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\alias{ab_ddd}
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\alias{ab_ddd_units}
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\alias{ab_info}
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\alias{ab_url}
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\alias{set_ab_names}
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\title{Get Properties of an Antibiotic}
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\usage{
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ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
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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_AMR_locale(), ...)
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ab_atc(x, only_first = FALSE, ...)
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ab_atc_group1(x, language = get_AMR_locale(), ...)
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ab_atc_group2(x, language = get_AMR_locale(), ...)
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ab_loinc(x, ...)
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ab_ddd(x, administration = "oral", ...)
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ab_ddd_units(x, administration = "oral", ...)
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ab_info(x, language = get_AMR_locale(), ...)
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ab_url(x, open = FALSE, ...)
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ab_property(x, property = "name", language = get_AMR_locale(), ...)
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set_ab_names(
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data,
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...,
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property = "name",
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language = get_AMR_locale(),
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snake_case = NULL
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)
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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 antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
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\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
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\item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
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\item{...}{in case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}}
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\item{only_first}{a \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)}
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\item{administration}{way of administration, either \code{"oral"} or \code{"iv"}}
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\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
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\item{property}{one of the column names of one of the \link{antibiotics} data set: \code{vector_or(colnames(antibiotics), sort = FALSE)}.}
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\item{data}{a \link{data.frame} of which the columns need to be renamed, or a \link{character} vector of column names}
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\item{snake_case}{a \link{logical} to indicate whether the names should be in so-called \href{https://en.wikipedia.org/wiki/Snake_case}{snake case}: in lower case and all spaces/slashes replaced with an underscore (\verb{_})}
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}
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\value{
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\itemize{
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\item An \link{integer} in case of \code{\link[=ab_cid]{ab_cid()}}
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\item A named \link{list} in case of \code{\link[=ab_info]{ab_info()}} and multiple \code{\link[=ab_atc]{ab_atc()}}/\code{\link[=ab_synonyms]{ab_synonyms()}}/\code{\link[=ab_tradenames]{ab_tradenames()}}
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\item A \link{double} in case of \code{\link[=ab_ddd]{ab_ddd()}}
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\item A \link{data.frame} in case of \code{\link[=set_ab_names]{set_ab_names()}}
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\item A \link{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 \link{antibiotics} data set. All input values will be evaluated internally with \code{\link[=as.ab]{as.ab()}}.
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}
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\details{
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All output \link[=translate]{will be translated} where possible.
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The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
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The function \code{\link[=set_ab_names]{set_ab_names()}} is a special column renaming function for \link{data.frame}s. It renames columns names that resemble antimicrobial drugs. It always makes sure that the new column names are unique. If \code{property = "atc"} is set, preference is given to ATC codes from the J-group.
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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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European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm}
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}
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\section{Reference Data Publicly Available}{
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All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
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}
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\examples{
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# all properties:
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ab_name("AMX")
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ab_atc("AMX")
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ab_cid("AMX")
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ab_synonyms("AMX")
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ab_tradenames("AMX")
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ab_group("AMX")
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ab_atc_group1("AMX")
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ab_atc_group2("AMX")
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ab_url("AMX")
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# smart lowercase transformation
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ab_name(x = c("AMC", "PLB"))
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ab_name(x = c("AMC", "PLB"), tolower = TRUE)
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# defined daily doses (DDD)
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ab_ddd("AMX", "oral")
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ab_ddd_units("AMX", "oral")
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ab_ddd("AMX", "iv")
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ab_ddd_units("AMX", "iv")
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ab_info("AMX") # all properties as a list
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# all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
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ab_atc("AMP")
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ab_group("J01CA01")
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ab_loinc("ampicillin")
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ab_name("21066-6")
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ab_name(6249)
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ab_name("J01CA01")
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# spelling from different languages and dyslexia are no problem
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ab_atc("ceftriaxon")
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ab_atc("cephtriaxone")
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ab_atc("cephthriaxone")
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ab_atc("seephthriaaksone")
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# use set_ab_names() for renaming columns
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colnames(example_isolates)
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colnames(set_ab_names(example_isolates))
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colnames(set_ab_names(example_isolates, NIT:VAN))
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\donttest{
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if (require("dplyr")) {
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example_isolates \%>\%
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set_ab_names()
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# this does the same:
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example_isolates \%>\%
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rename_with(set_ab_names)
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# set_ab_names() works with any AB property:
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example_isolates \%>\%
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set_ab_names(property = "atc")
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example_isolates \%>\%
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set_ab_names(where(is.sir)) \%>\%
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colnames()
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example_isolates \%>\%
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set_ab_names(NIT:VAN) \%>\%
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colnames()
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}
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}
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}
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\seealso{
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\link{antibiotics}
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}
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