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AMR
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atc_ functions

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dr. M.S. (Matthijs) Berends 2019-01-27 10:53:59 +01:00
parent b39055c018
commit 6ec940bc75
6 changed files with 21 additions and 18 deletions
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3
.gitlab-ci.yml
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@ -27,6 +27,9 @@ stages:
# debian stretch only contains R 3.3...
image: debian:buster-slim
variables:
WARNINGS_ARE_ERRORS: 1
before_script:
- apt-get update -qq
# install dependencies for packages

6
R/whocc.R
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@ -19,7 +19,7 @@
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' WHO Collaborating Centre for Drug Statistics Methodology
#' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology
#'
#' All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
#' @section WHOCC:
@ -34,7 +34,7 @@
#' @rdname WHOCC
#' @examples
#' as.atc("meropenem")
#' ab_name("J01DH02")
#' atc_name("J01DH02")
#'
#' ab_tradenames("flucloxacillin")
#' atc_tradenames("flucloxacillin")
NULL

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README.md
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@ -1,4 +1,4 @@
# `AMR` (for R) <img src="man/figures/logo.png" align="right" height="120px" />
# `AMR` (for R) <img src="docs/logo.png" align="right" height="120px" />
### Not a developer? Then please visit our website [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR) to read about this package.
**It contains documentation about all of the included functions and also a comprehensive tutorial about how to conduct AMR analysis.**
@ -22,11 +22,11 @@ Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https
<sup>a</sup> Thesis dissertant<br>
<sup>b</sup> Thesis advisor
<a href="https://www.rug.nl"><img src="man/figures/logo_rug.png" height="60px"></a>
<a href="https://www.umcg.nl"><img src="man/figures/logo_umcg.png" height="60px"></a>
<a href="https://www.certe.nl"><img src="man/figures/logo_certe.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_eh1h.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
<a href="https://www.rug.nl"><img src="docs/logo_rug.png" height="60px"></a>
<a href="https://www.umcg.nl"><img src="docs/logo_umcg.png" height="60px"></a>
<a href="https://www.certe.nl"><img src="docs/logo_certe.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="docs/logo_eh1h.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="docs/logo_interreg.png" height="60px"></a>
## How to get this package
All stable versions of this package [are published on CRAN](https://CRAN.R-project.org/package=AMR), the official R network with a peer-reviewed submission process.

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docs/reference/WHOCC.html
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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
<title>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,7 +45,7 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:title" content="WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC" />
<meta property="og:description" content="All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology." />
@ -216,7 +216,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>WHO Collaborating Centre for Drug Statistics Methodology</h1>
<h1>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</h1>
<div class="hidden name"><code>WHOCC.Rd</code></div>
</div>
@ -246,9 +246,9 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># NOT RUN {</span>
<span class='fu'><a href='as.atc.html'>as.atc</a></span>(<span class='st'>"meropenem"</span>)
<span class='fu'><a href='AMR-deprecated.html'>ab_name</a></span>(<span class='st'>"J01DH02"</span>)
<span class='fu'><a href='atc_property.html'>atc_name</a></span>(<span class='st'>"J01DH02"</span>)
<span class='fu'><a href='AMR-deprecated.html'>ab_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
<span class='fu'><a href='atc_property.html'>atc_tradenames</a></span>(<span class='st'>"flucloxacillin"</span>)
<span class='co'># }</span></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

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docs/reference/index.html
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@ -249,7 +249,7 @@
<td>
<p><code><a href="WHOCC.html">WHOCC</a></code> </p>
</td>
<td><p>WHO Collaborating Centre for Drug Statistics Methodology</p></td>
<td><p>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology</p></td>
</tr>
</tbody><tbody>
<tr>

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man/WHOCC.Rd
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@ -2,7 +2,7 @@
% Please edit documentation in R/whocc.R
\name{WHOCC}
\alias{WHOCC}
\title{WHO Collaborating Centre for Drug Statistics Methodology}
\title{WHOCC: WHO Collaborating Centre for Drug Statistics Methodology}
\description{
All antimicrobial drugs and their official names, ATC codes, ATC groups and defined daily dose (DDD) are included in this package, using the WHO Collaborating Centre for Drug Statistics Methodology.
}
@ -24,7 +24,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
\examples{
as.atc("meropenem")
ab_name("J01DH02")
atc_name("J01DH02")
ab_tradenames("flucloxacillin")
atc_tradenames("flucloxacillin")
}