big website update, licence txt update

docs/reference/AMR-deprecated.html

@@ -49,7 +49,7 @@
 
 <meta property="og:description" content="These functions are 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 Using the functions will give a warning with the name of the function it has been replaced by." />
 
-<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>
      
@@ -169,12 +222,20 @@
 
     <pre class="usage"><span class='fu'>ratio</span>(<span class='no'>x</span>, <span class='no'>ratio</span>)</pre>
         
+    <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>
+    
 
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
-                </ul>
+      
+      <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
+          </ul>
 
   </div>
 </div>