mirror of https://github.com/msberends/AMR.git
91 lines
3.4 KiB
R
91 lines
3.4 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/atc_online.R
|
|
\name{atc_online_property}
|
|
\alias{atc_online_property}
|
|
\alias{atc_online_groups}
|
|
\alias{atc_online_ddd}
|
|
\title{Get ATC properties from WHOCC website}
|
|
\source{
|
|
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
|
|
}
|
|
\usage{
|
|
atc_online_property(
|
|
atc_code,
|
|
property,
|
|
administration = "O",
|
|
url = "https://www.whocc.no/atc_ddd_index/?code=\%s&showdescription=no"
|
|
)
|
|
|
|
atc_online_groups(atc_code, ...)
|
|
|
|
atc_online_ddd(atc_code, ...)
|
|
}
|
|
\arguments{
|
|
\item{atc_code}{a character or character vector with ATC code(s) of antibiotic(s)}
|
|
|
|
\item{property}{property of an ATC code. Valid values are \code{"ATC"}, \code{"Name"}, \code{"DDD"}, \code{"U"} (\code{"unit"}), \code{"Adm.R"}, \code{"Note"} and \code{groups}. For this last option, all hierarchical groups of an ATC code will be returned, see Examples.}
|
|
|
|
\item{administration}{type of administration when using \code{property = "Adm.R"}, see Details}
|
|
|
|
\item{url}{url of website of the WHO. The sign \verb{\%s} can be used as a placeholder for ATC codes.}
|
|
|
|
\item{...}{parameters to pass on to \code{atc_property}}
|
|
}
|
|
\description{
|
|
Gets data from the WHO to determine properties of an ATC (e.g. an antibiotic) like name, defined daily dose (DDD) or standard unit.
|
|
|
|
\strong{This function requires an internet connection.}
|
|
}
|
|
\details{
|
|
Options for parameter \code{administration}:
|
|
\itemize{
|
|
\item \code{"Implant"} = Implant
|
|
\item \code{"Inhal"} = Inhalation
|
|
\item \code{"Instill"} = Instillation
|
|
\item \code{"N"} = nasal
|
|
\item \code{"O"} = oral
|
|
\item \code{"P"} = parenteral
|
|
\item \code{"R"} = rectal
|
|
\item \code{"SL"} = sublingual/buccal
|
|
\item \code{"TD"} = transdermal
|
|
\item \code{"V"} = vaginal
|
|
}
|
|
|
|
Abbreviations of return values when using \code{property = "U"} (unit):
|
|
\itemize{
|
|
\item \code{"g"} = gram
|
|
\item \code{"mg"} = milligram
|
|
\item `"mcg"`` = microgram
|
|
\item \code{"U"} = unit
|
|
\item \code{"TU"} = thousand units
|
|
\item \code{"MU"} = million units
|
|
\item \code{"mmol"} = millimole
|
|
\item \code{"ml"} = milliliter (e.g. eyedrops)
|
|
}
|
|
}
|
|
\section{Questioning lifecycle}{
|
|
|
|
\if{html}{\figure{lifecycle_questioning.svg}{options: style=margin-bottom:5px} \cr}
|
|
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{questioning}. We are no longer convinced that this function is the optimal approach (but we do not know yet what a better approach would be), or whether this function should be in our \code{AMR} package at all.
|
|
}
|
|
|
|
\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 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}.
|
|
}
|
|
|
|
\examples{
|
|
\dontrun{
|
|
# oral DDD (Defined Daily Dose) of amoxicillin
|
|
atc_online_property("J01CA04", "DDD", "O")
|
|
# parenteral DDD (Defined Daily Dose) of amoxicillin
|
|
atc_online_property("J01CA04", "DDD", "P")
|
|
|
|
atc_online_property("J01CA04", property = "groups") # search hierarchical groups of amoxicillin
|
|
# [1] "ANTIINFECTIVES FOR SYSTEMIC USE"
|
|
# [2] "ANTIBACTERIALS FOR SYSTEMIC USE"
|
|
# [3] "BETA-LACTAM ANTIBACTERIALS, PENICILLINS"
|
|
# [4] "Penicillins with extended spectrum"
|
|
}
|
|
}
|