From f39815aa87272849f8e0c808099c4cee780c2a81 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 3 Nov 2016 14:33:05 +0100
Subject: Static documentation rebuilt by pkgdown::build_site()

Using pkgdown with PR hadley/pkgdown#212
---
 docs/reference/index.html | 159 +++++++++++++++++++++++++---------------------
 1 file changed, 85 insertions(+), 74 deletions(-)

(limited to 'docs/reference/index.html')

diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6fcf39c8..23eb608b 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,7 +60,12 @@
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
-        
+        <li>
+  <a href="http://github.com/jranke/mkin">
+    <span class="fa fa-github fa-lg"></span>
+     
+  </a>
+</li>
       </ul>
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
@@ -80,175 +85,180 @@
       <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2>
       <p class="section-desc"><p>Essential functionality</p></p>
 
-      <p><a href="mkinfit.html">
-</a></p>
+      
+      <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p>
       <ul>
         <li><code><a href="mkinfit.html">mkinfit</a></code></li>
       </ul>
-      <p><a href="mkinmod.html">
-</a></p>
+      
+      <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p>
       <ul>
         <li><code><a href="mkinmod.html">mkinmod</a></code></li>
       </ul>
-      <p><a href="mmkin.html">
-</a></p>
+      
+      <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p>
       <ul>
         <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>
+      
+      <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
       <ul>
         <li><code><a href="endpoints.html">endpoints</a></code></li>
       </ul>
-      <p><a href="mkinerrmin.html">
-</a></p>
+      
+      <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
       <ul>
         <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
       </ul>
-      <p><a href="mkinparplot.html">
-</a></p>
+      
+      <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
+    mkinfit</a></p>
       <ul>
         <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
       </ul>
-      <p><a href="mkinresplot.html">
-</a></p>
+      
+      <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</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>
+      
+      <p><a href="plot.mmkin.html">Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</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>
+      
+      <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</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>
+      
+      <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</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>
+      
+      <p><a href="FOCUS_2006_HS_ref_A_to_F.html">Results of fitting the HS model to Datasets A to F of FOCUS (2006)</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>
+      
+      <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</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>
+      
+      <p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</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>
+      
+      <p><a href="mkinds.html">A dataset class for mkin</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>
+        <li><code><a href="mkinds.html">mkinds</a></code></li>
       </ul>
-      <p><a href="synthetic_data_for_UBA.html">
-</a></p>
+      
+      <p><a href="print.mkinds.html">Print mkinds objects</a></p>
+      <ul>
+        <li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
+      </ul>
+      
+      <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</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>
+      
+      <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>
+      
+      <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p>
       <ul>
-        <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
+        <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
       </ul>
-      <p><a href="mkin_long_to_wide.html">
-</a></p>
+      
+      <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
       <ul>
-        <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+        <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
       </ul>
-      <p><a href="mkinpredict.html">
-</a></p>
+      
+      <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p>
       <ul>
         <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
       </ul>
-      <p><a href="mkinsub.html">
-</a></p>
+      
+      <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</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>
+      
+      <p><a href="print.mkinmod.html">Print mkinmod objects</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>
+      
+      <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</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>
+      
+      <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>
+      
+      <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>
+      
+      <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>
+      
+      <p><a href="SFO.solution.html">Single First-Order kinetics</a></p>
+      <ul>
+        <li><code><a href="SFO.solution.html">SFO.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-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2>
+      <p class="section-desc"></p>
+
+      
+      <p><a href="add_err.html">Add normally distributed errors to simulated kinetic degradation data</a></p>
+      <ul>
+        <li><code><a href="add_err.html">add_err</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>
+      
+      <p><a href="mkinplot.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
       <ul>
         <li><code><a href="mkinplot.html">mkinplot</a></code></li>
       </ul>
@@ -265,6 +275,7 @@
       <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-generate-synthetic-datasets">Generate synthetic datasets</a></li>
       <li><a href="#section-deprecated-functions">Deprecated functions</a></li>
     </ul>
   </div>
@@ -272,7 +283,7 @@
 
       <footer>
       <div class="copyright">
-  <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+  <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-- 
cgit v1.2.1