Static documentation rebuilt by pkgdown::build_site()

Using pkgdown with PR hadley/pkgdown#212

1 files changed, 19 insertions, 20 deletions

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index ab5ce062..ccd56ca4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -61,7 +61,12 @@
       </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 -->
@@ -83,7 +88,7 @@
   constants and other paramters that can only take on positive values, a
   simple log transformation is used. For compositional parameters, such as
   the formations fractions that should always sum up to 1 and can not be
-  negative, the <code><a href='ilr.html'>ilr</a></code> transformation is used.</p>
+  negative, the <code>ilr</code> transformation is used.</p>
 
     <p>The transformation of sets of formation fractions is fragile, as it supposes
   the same ordering of the components in forward and backward transformation.
@@ -109,7 +114,7 @@
       <dd>
     The kinetic model of class <code><a href='mkinmod.html'>mkinmod</a></code>, containing the names of
     the model variables that are needed for grouping the formation fractions
-    before <code><a href='ilr.html'>ilr</a></code> transformation, the parameter names and 
+    before <code>ilr</code> transformation, the parameter names and 
     the information if the pathway to sink is included in the model. 
   </dd>
       <dt>transform_rates</dt>
@@ -128,7 +133,7 @@
     assumption of normal distribution of the estimator. The default (TRUE) is 
     to do transformations. The g parameter of the DFOP and HS models are also 
     transformed, as they can also be seen as compositional data. The
-    transformation used for these transformations is the <code><a href='ilr.html'>ilr</a></code>
+    transformation used for these transformations is the <code>ilr</code>
     transformation.
   </dd>
     </dl>
@@ -139,18 +144,15 @@
   as the original parameters.</p>
     
 
-    <h2 class="hasAnchor" id="examples">
-      <a class="anchor" href="#examples"></a>
-      Examples
-    </h2>
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
   <span class='kw'>parent</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'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
-  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
+  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version:    0.9.44.9000 
-#&gt; R version:       3.3.1 
-#&gt; Date of fit:     Wed Oct 26 23:50:51 2016 
-#&gt; Date of summary: Wed Oct 26 23:50:51 2016 
+#&gt; R version:       3.3.2 
+#&gt; Date of fit:     Thu Nov  3 17:46:36 2016 
+#&gt; Date of summary: Thu Nov  3 17:46:36 2016 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +160,7 @@
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted with method Port using 153 model solutions performed in 0.629 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.657 s
 #&gt; 
 #&gt; Weighting: none
 #&gt; 
@@ -221,8 +223,7 @@
 #&gt; Estimated disappearance times:
 #&gt;           DT50   DT90
 #&gt; parent   7.023  23.33
-#&gt; m1     131.761 437.70
-#&gt; </div><div class='input'>
+#&gt; m1     131.761 437.70</div><div class='input'>
 <span class='co'>## Not run: ------------------------------------</span>
 <span class='co'># fit.2 &lt;- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span>
 <span class='co'># summary(fit.2, data=FALSE) </span>
@@ -233,10 +234,8 @@
 <span class='no'>transformed</span> <span class='kw'>&lt;-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span>
 <span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'>&lt;-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)
 <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt;          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
-#&gt;        100.750000         -2.302585         -2.301586         -2.300587 
-#&gt; </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
-#&gt;      100.7500        0.1000        0.1001        0.1002 
-#&gt; </div><div class='input'>
+#&gt;        100.750000         -2.302585         -2.301586         -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
+#&gt;      100.7500        0.1000        0.1001        0.1002 </div><div class='input'>
 <span class='co'>## Not run: ------------------------------------</span>
 <span class='co'># # The case of formation fractions</span>
 <span class='co'># SFO_SFO.ff &lt;- mkinmod(</span>
@@ -280,7 +279,7 @@
 
       <footer>
       <div class="copyright">
-  <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+  <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">