From c6086d1dd97ad2d6420625de7b8009b1b0f85d06 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 18 Nov 2016 15:01:53 +0100
Subject: Static documentation rebuilt by pkgdown::build_site(run_dont_run =
 TRUE)

Using branch 'jranke' on jranke/pkgdown, fixing issues
hadley/pgkdown#178 and hadley/pkgdown#213

Remove plot=TRUE from mkinfit calls also in dontrun sections of examples
to avoid a flood png files documenting the progress of the fit.
---
 docs/reference/index.html | 91 +++++++++++++++++++++++++----------------------
 1 file changed, 48 insertions(+), 43 deletions(-)

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

diff --git a/docs/reference/index.html b/docs/reference/index.html
index 32455baa..2d052a80 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -86,14 +86,14 @@
       <p class="section-desc"><p>Essential functionality</p></p>
 
       
-      <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</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="mkinfit.html">mkinfit</a></code></li>
+        <li><code><a href="mkinmod.html">mkinmod</a></code></li>
       </ul>
       
-      <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</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="mkinmod.html">mkinmod</a></code></li>
+        <li><code><a href="mkinfit.html">mkinfit</a></code></li>
       </ul>
       
       <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p>
@@ -104,35 +104,35 @@
       <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
 
       
-      <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
+      <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
       <ul>
-        <li><code><a href="endpoints.html">endpoints</a></code></li>
+        <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="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
+      <p><a href="summary.mkinfit.html">Summary method for class &quot;mkinfit&quot;</a></p>
       <ul>
-        <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
+        <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>
       
-      <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
-  list(list(&quot;mkinfit&quot;))</a></p>
+      <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
       <ul>
-        <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
+        <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
       </ul>
       
-      <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
+      <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
+  list(list(&quot;mkinfit&quot;))</a></p>
       <ul>
-        <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
+        <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
       </ul>
       
-      <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</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="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
+        <li><code><a href="endpoints.html">endpoints</a></code></li>
       </ul>
       
-      <p><a href="summary.mkinfit.html">Summary method for class &quot;mkinfit&quot;</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="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
+        <li><code><a href="mkinerrmin.html">mkinerrmin</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>
@@ -151,9 +151,14 @@
       <p class="section-desc"></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>
+      <p><a href="FOCUS_2006_datasets.html">Datasets A to F from the FOCUS Kinetics report from 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>
+        <li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code></li>
+      </ul>
+      
+      <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="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p>
@@ -166,9 +171,9 @@
         <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">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</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_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
+        <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="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p>
@@ -176,47 +181,47 @@
         <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
       </ul>
       
-      <p><a href="mkinds.html">A dataset class for mkin</a></p>
+      <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p>
       <ul>
-        <li><code><a href="mkinds.html">mkinds</a></code></li>
+        <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="print.mkinds.html">Print mkinds objects</a></p>
+      <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p>
       <ul>
-        <li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
+        <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
       </ul>
       
-      <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</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">Synthetic datasets for one parent compound with two metabolites</a></p>
+      <p><a href="print.mkinds.html">Print mkinds objects</a></p>
       <ul>
-        <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
+        <li><code><a href="print.mkinds.html">print.mkinds</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="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
       <ul>
-        <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
+        <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
       </ul>
       
-      <p><a href="ilr.html">Function to perform isometric log-ratio transformation</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">Convert a dataframe from long to wide format</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="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
+        <li><code><a href="mkinsub.html">mkinsub</a></code></li>
       </ul>
       
-      <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
+      <p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
       <ul>
-        <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
+        <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
       </ul>
       
       <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p>
@@ -224,19 +229,19 @@
         <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
       </ul>
       
-      <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p>
+      <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
       <ul>
-        <li><code><a href="mkinsub.html">mkinsub</a></code></li>
+        <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>
       
-      <p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
+      <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p>
       <ul>
-        <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
+        <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
       </ul>
       
-      <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
+      <p><a href="geometric_mean.html">Calculate the geometric mean</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>
+        <li><code><a href="geometric_mean.html">geometric_mean</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>
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