Complete pkgdown conf, rerun with current master branch

1 files changed, 165 insertions, 8 deletions

diff --git a/docs/reference/index.html b/docs/reference/index.html
index 60d11171..6fcf39c8 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -49,20 +49,18 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../index.html">Home</a>
+  <a href="../reference/index.html">Reference</a>
 </li>
 <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+  <a href="../news/index.html">News</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="https://github.com/jranke/mkin">
-    <span class="fa fa-github fa-lg"></span>
-     
-  </a>
-</li>
+        
       </ul>
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
@@ -98,8 +96,162 @@
         <li><code><a href="mmkin.html">mmkin</a></code></li>
       </ul>
           <h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2>
+      <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
+
+      <p><a href="endpoints.html">
+</a></p>
+      <ul>
+        <li><code><a href="endpoints.html">endpoints</a></code></li>
+      </ul>
+      <p><a href="mkinerrmin.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
+      </ul>
+      <p><a href="mkinparplot.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
+      </ul>
+      <p><a href="mkinresplot.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
+      </ul>
+      <p><a href="plot.mkinfit.html">
+</a></p>
+      <ul>
+        <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
+      </ul>
+      <p><a href="summary.mkinfit.html">
+</a></p>
+      <ul>
+        <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
+      </ul>
+          <h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
+      <p class="section-desc"><p>Functions working with aggregated results</p></p>
+
+      <p><a href="Extract.mmkin.html">Subsetting method for mmkin objects</a></p>
+      <ul>
+        <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li>
+      </ul>
+      <p><a href="plot.mmkin.html">
+</a></p>
+      <ul>
+        <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li>
+      </ul>
+          <h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2>
       <p class="section-desc"></p>
 
+      <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">
+</a></p>
+      <ul>
+        <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
+      </ul>
+      <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">
+</a></p>
+      <ul>
+        <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li>
+      </ul>
+      <p><a href="FOCUS_2006_HS_ref_A_to_F.html">
+</a></p>
+      <ul>
+        <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
+      </ul>
+      <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">
+</a></p>
+      <ul>
+        <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
+      </ul>
+      <p><a href="mccall81_245T.html">
+</a></p>
+      <ul>
+        <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
+      </ul>
+      <p><a href="schaefer07_complex_case.html">
+</a></p>
+      <ul>
+        <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
+      </ul>
+      <p><a href="synthetic_data_for_UBA.html">
+</a></p>
+      <ul>
+        <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
+      </ul>
+          <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
+      <p class="section-desc"></p>
+
+      <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p>
+      <ul>
+        <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
+      </ul>
+      <p><a href="ilr.html">
+</a></p>
+      <ul>
+        <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
+      </ul>
+      <p><a href="mkin_long_to_wide.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+      </ul>
+      <p><a href="mkinpredict.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
+      </ul>
+      <p><a href="mkinsub.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinsub.html">mkinsub</a></code></li>
+      </ul>
+      <p><a href="mkin_wide_to_long.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
+      </ul>
+      <p><a href="print.mkinmod.html">
+</a></p>
+      <ul>
+        <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
+      </ul>
+      <p><a href="transform_odeparms.html">
+</a></p>
+      <ul>
+        <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
+      </ul>
+          <h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
+      <p class="section-desc"><p>Parent only model solutions</p></p>
+
+      <p><a href="DFOP.solution.html">
+</a></p>
+      <ul>
+        <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
+      </ul>
+      <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p>
+      <ul>
+        <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
+      </ul>
+      <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p>
+      <ul>
+        <li><code><a href="HS.solution.html">HS.solution</a></code></li>
+      </ul>
+      <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p>
+      <ul>
+        <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
+      </ul>
+      <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p>
+      <ul>
+        <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
+      </ul>
+          <h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
+      <p class="section-desc"><p>Functions that have been superseeded</p></p>
+
+      <p><a href="mkinplot.html">
+</a></p>
+      <ul>
+        <li><code><a href="mkinplot.html">mkinplot</a></code></li>
+      </ul>
     
     </div>
   </div>
@@ -109,6 +261,11 @@
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#section-main-functions">Main functions</a></li>
       <li><a href="#section-show-results">Show results</a></li>
+      <li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
+      <li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
+      <li><a href="#section-helper-functions">Helper functions</a></li>
+      <li><a href="#section-analytical-solutions">Analytical solutions</a></li>
+      <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
     </ul>
   </div>
 </div>