Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge

3 files changed, 21 insertions, 26 deletions

diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index a84b8c94..1234de20 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 3d92a7b8..92919da9 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>
@@ -104,19 +99,19 @@ 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 4920.5498 4957.8305 5073.8005 4995.1112 5150.4259
-## Eigenvalue based       792.7603  820.6244  849.2773  848.4885  877.5358
-## deSolve, compiled      663.5431  673.4949  678.4844  683.4468  685.9551
+## deSolve, not compiled 9307.3194 9319.9546 9332.8171 9332.5899 9345.5659
+## Eigenvalue based       855.3608  855.8081  869.4725  856.2555  876.5283
+## deSolve, compiled      686.6143  687.9256  698.0279  689.2369  703.7346
 ##                             max neval cld
-## deSolve, not compiled 5305.7406     3   b
-## Eigenvalue based       906.5832     3  a 
-## deSolve, compiled      688.4634     3  a</code></pre>
-<p>We see that using the compiled model is by a factor of 7.3 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 9358.5420     3   c
+## Eigenvalue based       896.8012     3  b 
+## deSolve, compiled      718.2324     3 a</code></pre>
+<p>We see that using the compiled model is by a factor of 13.5 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 7.308706
-## Eigenvalue based      1.241484
-## deSolve, compiled     1.000000</code></pre>
+<pre><code>##                          median
+## deSolve, not compiled 13.540468
+## Eigenvalue based       1.242324
+## deSolve, compiled      1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
 <h2>Benchmark for a model that can not be solved with Eigenvalues</h2>
@@ -133,17 +128,17 @@ 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 10.710141 10.757988 10.810178 10.805835 10.860196
-## deSolve, compiled      1.200581  1.203966  1.211877  1.207351  1.217525
+## deSolve, not compiled 20.130709 20.147223 20.180429 20.163737 20.205289
+## deSolve, compiled      1.235864  1.255748  1.267458  1.275632  1.283255
 ##                             max neval cld
-## deSolve, not compiled 10.914558     3   b
-## deSolve, compiled      1.227699     3  a</code></pre>
+## deSolve, not compiled 20.246841     3   b
+## deSolve, compiled      1.290878     3  a</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 8.950036
-## deSolve, compiled     1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code using the inline package!</p>
-<p>This vignette was built with mkin 0.9.40.900 on</p>
+## deSolve, not compiled 15.80686
+## deSolve, compiled      1.00000</code></pre>
+<p>Here we get a performance benefit of a factor of 15.8 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>This vignette was built with mkin 0.9.41 on</p>
 <pre><code>## R version 3.2.2 (2015-08-14)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)</code></pre>
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index ce628c0e..9c1a03f3 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf