Merge branch 'master' of kolab:mkin

1 files changed, 16 insertions, 24 deletions

diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 605f572e..6c53f805 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -18,12 +18,21 @@
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+<!-- clipboard.js -->
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 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
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+  
+  
+<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" />
 
+<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the
+  software quality of KinGUI in the original publication (Schäfer et al., 2007).
+  The results from the fitting are also included." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -86,12 +95,7 @@
       </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 -->
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@@ -140,24 +144,12 @@
   <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
   <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
   <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
-  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+  <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  </div><span class='co'># NOT RUN {</span>
     <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-    <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='schaefer07_complex_case-4.png' alt='' width='540' height='400' /><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
-#&gt;   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
-#&gt;   0.3809618   0.1954667   0.4235715   0.0000000   0.4479596   0.5520404 
-#&gt; 
-#&gt; $SFORB
-#&gt; logical(0)
-#&gt; 
-#&gt; $distimes
-#&gt;            DT50      DT90
-#&gt; parent 13.95078  46.34349
-#&gt; A1     49.75345 165.27739
-#&gt; B1     37.26908 123.80521
-#&gt; C1     11.23130  37.30957
-#&gt; A2     28.50652  94.69662
-#&gt; </div><div class='input'>
- <span class='co'># Compare with the results obtained in the original publication</span>
+    <span class='fu'>plot</span>(<span class='no'>fit</span>)
+    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)
+
+<span class='co'># }</span><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span>
  <span class='fu'>print</span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt;         compound          parameter  KinGUI ModelMaker deviation
 #&gt; 1         parent   degradation rate  0.0496     0.0506       2.0
 #&gt; 2         parent               DT50 13.9900    13.6900       2.2
@@ -194,7 +186,7 @@
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-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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