big website update, licence txt update

docs/reference/microorganisms.html

@@ -49,7 +49,7 @@
 
 <meta property="og:description" content="A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa. MO codes can be looked up using as.mo." />
 
-<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
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-      <ul class="nav navbar-nav navbar-right">
-        <li>
+<li>
   <a href="../LICENSE-text.html">
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@@ -201,6 +254,12 @@ This package contains the <strong>complete microbial taxonomic data</strong> (wi
 <p>All (sub)species from <strong>the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package</strong>, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens. It also helps to quickly determine the Gram stain of bacteria, since all bacteria are classified into subkingdom Negibacteria or Posibacteria.</p>
 <p>ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].</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="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.umcg.html'>microorganisms.umcg</a></code></p></div>
@@ -217,6 +276,8 @@ This package contains the <strong>complete microbial taxonomic data</strong> (wi
 
       <li><a href="#itis">ITIS</a></li>
 
+      <li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
+
       <li><a href="#see-also">See also</a></li>
           </ul>