big website update, licence txt update

2025-07-25 06:15:47 +02:00 · 2019-01-02 23:24:07 +01:00
parent 4255707cb7
commit 6b2d464f8c
190 changed files with 8785 additions and 66176 deletions
--- a/docs/reference/abname.html
+++ b/docs/reference/abname.html
@ -49,7 +49,7 @@

 <meta property="og:description" content="Convert antibiotic codes to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from antibiotics." />

-<meta property="og:image" content="https://msberends.gitlab.io/logo.png" />
+<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary" />


@ -80,7 +80,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9008</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9009</span>
      </span>
    </div>

@ -93,12 +93,65 @@
    Home
  </a>
 </li>
-<li>
-  <a href="../articles/AMR.html">
-    <span class="fa fa-directions"></span>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    <span class="fa fa-question-circle"></span>
     
-    Get Started
+    How to
+     
+    <span class="caret"></span>
  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/AMR.html">
+        <span class="fa fa-directions"></span>
+         
+        Conduct AMR analysis
+      </a>
+    </li>
+    <li>
+      <a href="../articles/Predict.html">
+        <span class="fa fa-dice"></span>
+         
+        Predict antimicrobial resistance
+      </a>
+    </li>
+    <li>
+      <a href="../articles/EUCAST.html">
+        <span class="fa fa-exchange-alt"></span>
+         
+        Apply EUCAST rules
+      </a>
+    </li>
+    <li>
+      <a href="../articles/mo_property.html">
+        <span class="fa fa-bug"></span>
+         
+        Get properties of a microorganism
+      </a>
+    </li>
+    <li>
+      <a href="../articles/ab_property.html">
+        <span class="fa fa-capsules"></span>
+         
+        Get properties of an antibiotic
+      </a>
+    </li>
+    <li>
+      <a href="../articles/freq.html">
+        <span class="fa fa-sort-amount-down"></span>
+         
+        Create frequency tables
+      </a>
+    </li>
+    <li>
+      <a href="../articles/G_test.html">
+        <span class="fa fa-clipboard-check"></span>
+         
+        Use the G-test
+      </a>
+    </li>
+  </ul>
 </li>
 <li>
  <a href="../reference/">
@ -121,17 +174,17 @@
    Changelog
  </a>
 </li>
-<li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        <li>
  <a href="https://gitlab.com/msberends/AMR">
    <span class="fab fa fab fa-gitlab"></span>
     
    Source Code
  </a>
 </li>
-      </ul>
-      
-      <ul class="nav navbar-nav navbar-right">
-        <li>
+<li>
  <a href="../LICENSE-text.html">
    <span class="fa fa-book"></span>
     
@ -199,30 +252,44 @@

    <p><strong>The <code><a href='ab_property.html'>ab_property</a></code> functions are faster and more concise</strong>, but do not support concatenated strings, like <code>abname("AMCL+GENT"</code>.</p>
    
+    <h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
+
+    
+    <p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
+On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
+    

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>abname</span>(<span class='st'>"AMCL"</span>)</div><div class='output co'>#&gt; [1] "Amoxicillin and beta-lactamase inhibitor"</div><div class='input'><span class='co'># "Amoxicillin and beta-lactamase inhibitor"</span>
+    <pre class="examples"><span class='co'># NOT RUN {</span>
+<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>)
+<span class='co'># "Amoxicillin and beta-lactamase inhibitor"</span>

 <span class='co'># It is quite flexible at default (having `from = "guess"`)</span>
-<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"J01CA04"</span>, <span class='st'>"Trimox"</span>, <span class='st'>"dispermox"</span>, <span class='st'>"Amoxil"</span>))</div><div class='output co'>#&gt; [1] "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</div><div class='input'><span class='co'># "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</span>
+<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"amox"</span>, <span class='st'>"J01CA04"</span>, <span class='st'>"Trimox"</span>, <span class='st'>"dispermox"</span>, <span class='st'>"Amoxil"</span>))
+<span class='co'># "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin" "Amoxicillin"</span>

 <span class='co'># Multiple antibiotics can be combined with "+".</span>
 <span class='co'># The second antibiotic will be set to lower case when `tolower` was not set:</span>
-<span class='fu'>abname</span>(<span class='st'>"AMCL+GENT"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>"/"</span>)</div><div class='output co'>#&gt; [1] "Amoxicillin and beta-lactamase inhibitor/gentamicin"</div><div class='input'><span class='co'># "amoxicillin and enzyme inhibitor/gentamicin"</span>
+<span class='fu'>abname</span>(<span class='st'>"AMCL+GENT"</span>, <span class='kw'>textbetween</span> <span class='kw'>=</span> <span class='st'>"/"</span>)
+<span class='co'># "amoxicillin and enzyme inhibitor/gentamicin"</span>

-<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMCL"</span>, <span class='st'>"GENT"</span>))</div><div class='output co'>#&gt; [1] "Amoxicillin and beta-lactamase inhibitor"
-#&gt; [2] "Gentamicin"                              </div><div class='input'><span class='co'># "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"</span>
+<span class='fu'>abname</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"AMCL"</span>, <span class='st'>"GENT"</span>))
+<span class='co'># "Amoxicillin and beta-lactamase inhibitor" "Gentamicin"</span>

-<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"trivial_nl"</span>)</div><div class='output co'>#&gt; [1] "Amoxicilline/clavulaanzuur"</div><div class='input'><span class='co'># "Amoxicilline/clavulaanzuur"</span>
+<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"trivial_nl"</span>)
+<span class='co'># "Amoxicilline/clavulaanzuur"</span>

-<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"atc"</span>)</div><div class='output co'>#&gt; [1] "J01CR02"</div><div class='input'><span class='co'># "J01CR02"</span>
+<span class='fu'>abname</span>(<span class='st'>"AMCL"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"atc"</span>)
+<span class='co'># "J01CR02"</span>

 <span class='co'># specific codes for University Medical Center Groningen (UMCG):</span>
-<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"umcg"</span>)</div><div class='output co'>#&gt; [1] "AMCL"</div><div class='input'><span class='co'># "AMCL"</span>
+<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"umcg"</span>)
+<span class='co'># "AMCL"</span>

 <span class='co'># specific codes for Certe:</span>
-<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"certe"</span>)</div><div class='output co'>#&gt; [1] "amcl"</div><div class='input'># "amcl"
-</div></pre>
+<span class='fu'>abname</span>(<span class='st'>"J01CR02"</span>, <span class='kw'>from</span> <span class='kw'>=</span> <span class='st'>"atc"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"certe"</span>)
+<span class='co'># "amcl"</span>
+<span class='co'># }</span></pre>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
@ -232,6 +299,8 @@
      <li><a href="#source">Source</a></li>

      <li><a href="#details">Details</a></li>
+
+      <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
      
      <li><a href="#examples">Examples</a></li>
    </ul>