% 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_cid} \alias{ab_synonyms} \alias{ab_tradenames} \alias{ab_group} \alias{ab_atc} \alias{ATC} \alias{ab_atc_group1} \alias{ab_atc_group2} \alias{ab_loinc} \alias{ab_ddd} \alias{ab_ddd_units} \alias{ab_info} \alias{ab_url} \alias{set_ab_names} \title{Get Properties of an Antibiotic} \usage{ ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...) ab_cid(x, ...) ab_synonyms(x, ...) ab_tradenames(x, ...) ab_group(x, language = get_AMR_locale(), ...) ab_atc(x, only_first = FALSE, ...) ab_atc_group1(x, language = get_AMR_locale(), ...) ab_atc_group2(x, language = get_AMR_locale(), ...) ab_loinc(x, ...) ab_ddd(x, administration = "oral", ...) ab_ddd_units(x, administration = "oral", ...) ab_info(x, language = get_AMR_locale(), ...) ab_url(x, open = FALSE, ...) ab_property(x, property = "name", language = get_AMR_locale(), ...) set_ab_names( data, ..., property = "name", language = get_AMR_locale(), snake_case = NULL ) } \arguments{ \item{x}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}} \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.} \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".} \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()}}} \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)} \item{administration}{way of administration, either \code{"oral"} or \code{"iv"}} \item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}} \item{property}{one of the column names of one of the \link{antibiotics} data set: \code{vector_or(colnames(antibiotics), sort = FALSE)}.} \item{data}{a \link{data.frame} of which the columns need to be renamed, or a \link{character} vector of column names} \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{_})} } \value{ \itemize{ \item An \link{integer} in case of \code{\link[=ab_cid]{ab_cid()}} \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()}} \item A \link{double} in case of \code{\link[=ab_ddd]{ab_ddd()}} \item A \link{data.frame} in case of \code{\link[=set_ab_names]{set_ab_names()}} \item A \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 \link[=translate]{will be translated} where possible. 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. 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. } \section{Source}{ World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://atcddd.fhi.no/atc_ddd_index/} European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: \url{https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm} } \section{Reference Data Publicly Available}{ 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}. } \examples{ # all properties: ab_name("AMX") ab_atc("AMX") ab_cid("AMX") ab_synonyms("AMX") ab_tradenames("AMX") ab_group("AMX") ab_atc_group1("AMX") ab_atc_group2("AMX") ab_url("AMX") # smart lowercase transformation ab_name(x = c("AMC", "PLB")) ab_name(x = c("AMC", "PLB"), tolower = TRUE) # defined daily doses (DDD) ab_ddd("AMX", "oral") ab_ddd_units("AMX", "oral") ab_ddd("AMX", "iv") ab_ddd_units("AMX", "iv") ab_info("AMX") # all properties as a list # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any': ab_atc("AMP") ab_group("J01CA01") ab_loinc("ampicillin") ab_name("21066-6") ab_name(6249) ab_name("J01CA01") # spelling from different languages and dyslexia are no problem ab_atc("ceftriaxon") ab_atc("cephtriaxone") ab_atc("cephthriaxone") ab_atc("seephthriaaksone") # use set_ab_names() for renaming columns colnames(example_isolates) colnames(set_ab_names(example_isolates)) colnames(set_ab_names(example_isolates, NIT:VAN)) \donttest{ if (require("dplyr")) { example_isolates \%>\% set_ab_names() # this does the same: example_isolates \%>\% rename_with(set_ab_names) # set_ab_names() works with any AB property: example_isolates \%>\% set_ab_names(property = "atc") example_isolates \%>\% set_ab_names(where(is.sir)) \%>\% colnames() example_isolates \%>\% set_ab_names(NIT:VAN) \%>\% colnames() } } } \seealso{ \link{antibiotics} }