mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 11:01:55 +02:00
atc_ functions
This commit is contained in:
@ -4,14 +4,38 @@
|
||||
\alias{AMR-deprecated}
|
||||
\alias{ratio}
|
||||
\alias{guess_mo}
|
||||
\alias{ab_property}
|
||||
\alias{ab_atc}
|
||||
\alias{ab_official}
|
||||
\alias{ab_name}
|
||||
\alias{ab_trivial_nl}
|
||||
\alias{ab_certe}
|
||||
\alias{ab_umcg}
|
||||
\alias{ab_tradenames}
|
||||
\title{Deprecated functions}
|
||||
\usage{
|
||||
ratio(x, ratio)
|
||||
|
||||
guess_mo(...)
|
||||
|
||||
ab_property(...)
|
||||
|
||||
ab_atc(...)
|
||||
|
||||
ab_official(...)
|
||||
|
||||
ab_name(...)
|
||||
|
||||
ab_trivial_nl(...)
|
||||
|
||||
ab_certe(...)
|
||||
|
||||
ab_umcg(...)
|
||||
|
||||
ab_tradenames(...)
|
||||
}
|
||||
\description{
|
||||
These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.
|
||||
These functions are so-called '\link{Deprecated}'. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
|
||||
@ -9,7 +9,7 @@ Welcome to the \code{AMR} package. This page gives some additional contact infor
|
||||
\details{
|
||||
This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods.
|
||||
|
||||
This package was created for academic research by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
This package was created for both academic research and routine analysis by PhD students of the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
|
||||
@ -1,59 +0,0 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/ab_property.R
|
||||
\name{ab_property}
|
||||
\alias{ab_property}
|
||||
\alias{ab_atc}
|
||||
\alias{ab_official}
|
||||
\alias{ab_name}
|
||||
\alias{ab_trivial_nl}
|
||||
\alias{ab_certe}
|
||||
\alias{ab_umcg}
|
||||
\alias{ab_tradenames}
|
||||
\title{Property of an antibiotic}
|
||||
\usage{
|
||||
ab_property(x, property = "official")
|
||||
|
||||
ab_atc(x)
|
||||
|
||||
ab_official(x, language = NULL)
|
||||
|
||||
ab_name(x, language = NULL)
|
||||
|
||||
ab_trivial_nl(x)
|
||||
|
||||
ab_certe(x)
|
||||
|
||||
ab_umcg(x)
|
||||
|
||||
ab_tradenames(x)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}}
|
||||
|
||||
\item{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}}
|
||||
|
||||
\item{language}{language of the returned text, defaults to English (\code{"en"}) and can be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).}
|
||||
}
|
||||
\value{
|
||||
A vector of values. In case of \code{ab_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
|
||||
}
|
||||
\description{
|
||||
Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
|
||||
}
|
||||
|
||||
\examples{
|
||||
ab_atc("amcl") # J01CR02
|
||||
ab_name("amcl") # Amoxicillin and beta-lactamase inhibitor
|
||||
ab_name("amcl", "nl") # Amoxicilline met enzymremmer
|
||||
ab_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
|
||||
ab_certe("amcl") # amcl
|
||||
ab_umcg("amcl") # AMCL
|
||||
}
|
||||
\seealso{
|
||||
\code{\link{antibiotics}}
|
||||
}
|
||||
73
man/atc_online.Rd
Normal file
73
man/atc_online.Rd
Normal file
@ -0,0 +1,73 @@
|
||||
% 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{Properties of an ATC code}
|
||||
\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 \code{\%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. \cr \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{\code{"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)}
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
\donttest{
|
||||
# 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"
|
||||
}
|
||||
}
|
||||
@ -1,77 +1,56 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/atc.R
|
||||
% Please edit documentation in R/atc_property.R
|
||||
\name{atc_property}
|
||||
\alias{atc_property}
|
||||
\alias{atc_groups}
|
||||
\alias{atc_ddd}
|
||||
\title{Properties of an ATC code}
|
||||
\source{
|
||||
\url{https://www.whocc.no/atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/}
|
||||
}
|
||||
\alias{atc_official}
|
||||
\alias{atc_name}
|
||||
\alias{atc_trivial_nl}
|
||||
\alias{atc_certe}
|
||||
\alias{atc_umcg}
|
||||
\alias{atc_tradenames}
|
||||
\title{Property of an antibiotic}
|
||||
\usage{
|
||||
atc_property(atc_code, property, administration = "O",
|
||||
url = "https://www.whocc.no/atc_ddd_index/?code=\%s&showdescription=no")
|
||||
atc_property(x, property = "official")
|
||||
|
||||
atc_groups(atc_code, ...)
|
||||
atc_official(x, language = NULL)
|
||||
|
||||
atc_ddd(atc_code, ...)
|
||||
atc_name(x, language = NULL)
|
||||
|
||||
atc_trivial_nl(x)
|
||||
|
||||
atc_certe(x)
|
||||
|
||||
atc_umcg(x)
|
||||
|
||||
atc_tradenames(x)
|
||||
}
|
||||
\arguments{
|
||||
\item{atc_code}{a character or character vector with ATC code(s) of antibiotic(s)}
|
||||
\item{x}{a (vector of a) valid \code{\link{atc}} code or any text that can be coerced to a valid atc with \code{\link{as.atc}}}
|
||||
|
||||
\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{property}{one of the column names of one of the \code{\link{antibiotics}} data set, like \code{"atc"} and \code{"official"}}
|
||||
|
||||
\item{administration}{type of administration when using \code{property = "Adm.R"}, see Details}
|
||||
|
||||
\item{url}{url of website of the WHO. The sign \code{\%s} can be used as a placeholder for ATC codes.}
|
||||
|
||||
\item{...}{parameters to pass on to \code{atc_property}}
|
||||
\item{language}{language of the returned text, defaults to English (\code{"en"}) and can be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English) or \code{"nl"} (Dutch).}
|
||||
}
|
||||
\value{
|
||||
A vector of values. In case of \code{atc_tradenames}, if \code{x} is of length one, a vector will be returned. Otherwise a \code{\link{list}}, with \code{x} as names.
|
||||
}
|
||||
\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. \cr \strong{This function requires an internet connection.}
|
||||
Use these functions to return a specific property of an antibiotic from the \code{\link{antibiotics}} data set, based on their ATC code. Get such a code with \code{\link{as.atc}}.
|
||||
}
|
||||
\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}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
|
||||
}
|
||||
|
||||
Abbreviations of return values when using \code{property = "U"} (unit):
|
||||
\itemize{
|
||||
\item{\code{"g"}}{ = gram}
|
||||
\item{\code{"mg"}}{ = milligram}
|
||||
\item{\code{"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)}
|
||||
}
|
||||
}
|
||||
\examples{
|
||||
\donttest{
|
||||
# What's the ATC of amoxicillin?
|
||||
guess_atc("Amoxicillin")
|
||||
# [1] "J01CA04"
|
||||
|
||||
# oral DDD (Defined Daily Dose) of amoxicillin
|
||||
atc_property("J01CA04", "DDD", "O")
|
||||
# parenteral DDD (Defined Daily Dose) of amoxicillin
|
||||
atc_property("J01CA04", "DDD", "P")
|
||||
|
||||
atc_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"
|
||||
as.atc("amcl") # J01CR02
|
||||
atc_name("amcl") # Amoxicillin and beta-lactamase inhibitor
|
||||
atc_name("amcl", "nl") # Amoxicilline met enzymremmer
|
||||
atc_trivial_nl("amcl") # Amoxicilline/clavulaanzuur
|
||||
atc_certe("amcl") # amcl
|
||||
atc_umcg("amcl") # AMCL
|
||||
}
|
||||
\seealso{
|
||||
\code{\link{antibiotics}}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user