From cc0d7a44cccac46ea1c71cf663aadee0efb2bba7 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 26 Jun 2015 16:08:04 +0200
Subject: Vignettes rebuilt by staticdocs::build_site() for static
 documentation on r-forge

---
 vignettes/compiled_models.html | 39 +++++++++++++++++----------------------
 1 file changed, 17 insertions(+), 22 deletions(-)

(limited to 'vignettes/compiled_models.html')

diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 12454559..a62f3826 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -82,13 +82,8 @@ img {
 <pre><code>##            gcc 
 ## &quot;/usr/bin/gcc&quot;</code></pre>
 <p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<pre class="r"><code>library(&quot;mkin&quot;)</code></pre>
-<pre><code>## Loading required package: minpack.lm
-## Loading required package: rootSolve
-## Loading required package: inline
-## Loading required package: methods
-## Loading required package: parallel</code></pre>
-<pre class="r"><code>SFO_SFO &lt;- mkinmod(
+<pre class="r"><code>library(&quot;mkin&quot;)
+SFO_SFO &lt;- mkinmod(
   parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
   m1 = mkinsub(&quot;SFO&quot;))</code></pre>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -104,18 +99,18 @@ smb.1 &lt;- summary(mb.1)[-1]
 rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
 print(smb.1)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517
-## Eigenvalue based       893.9459  921.1984  936.1750  948.4509  957.2895
-## deSolve, compiled      742.7723  745.4243  750.1963  748.0763  753.9083
+## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924
+## Eigenvalue based       901.5593  924.3357  968.8689  947.1121 1002.5238
+## deSolve, compiled      765.7604  770.7657  786.8638  775.7709  797.4156
 ##                             max neval
-## deSolve, not compiled 5466.1959     3
-## Eigenvalue based       966.1282     3
-## deSolve, compiled      759.7404     3</code></pre>
-<p>We see that using the compiled model is by a factor of 7.1 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
+## deSolve, not compiled 7204.1483     3
+## Eigenvalue based      1057.9355     3
+## deSolve, compiled      819.0602     3</code></pre>
+<p>We see that using the compiled model is by a factor of 9.2 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
 <pre class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 7.132304
-## Eigenvalue based      1.267853
+## deSolve, not compiled 9.176725
+## Eigenvalue based      1.220866
 ## deSolve, compiled     1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -133,16 +128,16 @@ smb.2 &lt;- summary(mb.2)[-1]
 rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
 print(smb.2)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 11.277340 11.336373 11.392883 11.395407 11.450654
-## deSolve, compiled      1.339204  1.342662  1.350783  1.346121  1.356573
+## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742
+## deSolve, compiled      1.467266  1.521451  1.555168  1.575636  1.599119
 ##                             max neval
-## deSolve, not compiled 11.505901     3
-## deSolve, compiled      1.367025     3</code></pre>
+## deSolve, not compiled 14.442561     3
+## deSolve, compiled      1.622601     3</code></pre>
 <pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 8.465368
+## deSolve, not compiled 9.100402
 ## deSolve, compiled     1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 8.5 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>Here we get a performance benefit of a factor of 9.1 using the version of the differential equation model compiled from C code using the inline package!</p>
 <p>This vignette was built with mkin 0.9.39 on</p>
 <pre><code>## R version 3.2.1 (2015-06-18)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
-- 
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