big website update, licence txt update

docs/reference/AMR.html

@@ -49,7 +49,7 @@
 
 <meta property="og:description" content="Welcome to the AMR package. This page gives some additional contact information about the authors." />
 
-<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>
      
@@ -173,10 +226,16 @@
     <p>This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and ti work with antibiotic properties by using evidence-based methods.</p>
 <p>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 &amp; Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG).</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="authors"><a class="anchor" href="#authors"></a>Authors</h2>
 
     
-    <p>Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2],  Corinna Glasner[1],  Alex W. Friedrich[1],  Bhanu Sinha[1] <br /></p>
+    <p>Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2],  Corinna Glasner[1],  Alex W. Friedrich[1],  Bhanu N.M. Sinha[1] <br /></p>
 <p>[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href='rug.nl'>rug.nl</a> <a href='umcg.nl'>umcg.nl</a> <br />
 [2] Certe Medical Diagnostics &amp; Advice, Groningen, the Netherlands - <a href='certe.nl'>certe.nl</a></p>
     
@@ -201,6 +260,8 @@ Post Office Box 30001 <br />
       
       <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="#authors">Authors</a></li>
 
       <li><a href="#contact-us">Contact us</a></li>