mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
181 lines
6.4 KiB
R
181 lines
6.4 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_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, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the 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://www.whocc.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 tranformation
|
|
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() \%>\%
|
|
head()
|
|
|
|
# this does the same:
|
|
example_isolates \%>\%
|
|
rename_with(set_ab_names) \%>\%
|
|
head()
|
|
|
|
# set_ab_names() works with any AB property:
|
|
example_isolates \%>\%
|
|
set_ab_names(property = "atc") \%>\%
|
|
head()
|
|
|
|
example_isolates \%>\%
|
|
set_ab_names(where(is.sir)) \%>\%
|
|
colnames()
|
|
|
|
example_isolates \%>\%
|
|
set_ab_names(NIT:VAN) \%>\%
|
|
colnames()
|
|
}
|
|
}
|
|
}
|
|
\seealso{
|
|
\link{antibiotics}
|
|
}
|