Another rebuild of the static docs

Now with rbenchmark installed, to get results for the compiled_models
vignette

1 files changed, 21 insertions, 16 deletions

diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 9f0b5708..915e5474 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -9,10 +9,7 @@
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-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin">
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@@ -80,7 +77,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-03-01</h4>
+            <h4 class="date">2018-03-09</h4>
           </div>
 
     
@@ -101,7 +98,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
 <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {
-  b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
+  b<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(
     <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,
                                       <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,
                                       <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
@@ -117,10 +114,15 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
   <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)
 }</code></pre></div>
 <pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
-<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
-<pre><code>## [1] "R package benchmark is not available"</code></pre>
-<p>We see that using the compiled model is by a factor of around NA 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><code>##                    test replications elapsed relative user.self sys.self
+## 3     deSolve, compiled            3   2.044    1.000     2.042        0
+## 1 deSolve, not compiled            3  14.198    6.946    14.185        0
+## 2      Eigenvalue based            3   2.751    1.346     2.747        0
+##   user.child sys.child
+## 3          0         0
+## 1          0         0
+## 2          0         0</code></pre>
+<p>We see that using the compiled model is by a factor of around 7 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>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
 <h2 class="hasAnchor">
@@ -131,7 +133,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
     <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),
     <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))
 
-  b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
+  b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(
     <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,
                                       <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
     <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
@@ -142,11 +144,14 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
   factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span>
   <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)
 }</code></pre></div>
-<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
-<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
-## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre>
-<pre><code>## [1] "R package benchmark is not available"</code></pre>
-<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p>
+<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<pre><code>##                    test replications elapsed relative user.self sys.self
+## 2     deSolve, compiled            3   3.695    1.000     3.692        0
+## 1 deSolve, not compiled            3  31.143    8.428    31.114        0
+##   user.child sys.child
+## 2          0         0
+## 1          0         0</code></pre>
+<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p>
 <p>This vignette was built with mkin 0.9.46.3 on</p>
 <pre><code>## R version 3.4.3 (2017-11-30)
 ## Platform: x86_64-pc-linux-gnu (64-bit)