atc_ functions

.gitlab-ci.yml

@@ -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

R/whocc.R

@@ -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

README.md

@@ -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.rug.nl"><img src="docs/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.umcg.nl"><img src="docs/logo_umcg.png" height="60px"></a>
-<a href="https://www.certe.nl"><img src="man/figures/logo_certe.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="man/figures/logo_eh1h.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="man/figures/logo_interreg.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.

docs/reference/WHOCC.html

@@ -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">

docs/reference/index.html

@@ -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>

man/WHOCC.Rd

@@ -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")
 }