Static documentation rebuilt using current pkgdown::build_site()

1 files changed, 29 insertions, 33 deletions

diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index d5d29a1a..9f0b5708 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -8,8 +8,11 @@
 <title>Performance benefit by using compiled model definitions in mkin • mkin</title>
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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@@ -77,7 +80,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-01-16</h4>
+            <h4 class="date">2018-03-01</h4>
           </div>
 
     
@@ -97,73 +100,66 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
   <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div>
 <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">if (<span class="kw">require</span>(rbenchmark)) {
+<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>(
-    <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_2006_D,
+    <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>),
-    <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D,
+    <span class="st">"Eigenvalue based"</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">"eigen"</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>(SFO_SFO, FOCUS_2006_D,
+    <span class="st">"deSolve, 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">quiet =</span> <span class="ot">TRUE</span>),
     <span class="dt">replications =</span> <span class="dv">3</span>)
   <span class="kw">print</span>(b<span class="fl">.1</span>)
   factor_SFO_SFO &lt;-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])
-} else {
+} <span class="cf">else</span> {
   factor_SFO_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>##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   1.940    1.000     1.940        0
-## 1 deSolve, not compiled            3  13.865    7.147    13.864        0
-## 2      Eigenvalue based            3   2.427    1.251     2.428        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>
+<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>
 </div>
 <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
 <h2 class="hasAnchor">
 <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2>
 <p>This evaluation is also taken from the example section of mkinfit.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">if (<span class="kw">require</span>(rbenchmark)) {
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {
   FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(
     <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>(
-    <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_2006_D,
+    <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_2006_D, <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>),
     <span class="dt">replications =</span> <span class="dv">3</span>)
   <span class="kw">print</span>(b<span class="fl">.2</span>)
   factor_FOMC_SFO &lt;-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])
-} else {
+} <span class="cf">else</span> {
   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>## 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   3.432    1.000     3.428        0
-## 1 deSolve, not compiled            3  28.844    8.404    28.840        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 0.9.47.1 on</p>
+<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>
+<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)
 ## Running under: Debian GNU/Linux 9 (stretch)</code></pre>
-<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre>
+<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre>
 </div>
 </div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
         <div id="tocnav">
-      <h2>Contents</h2>
+      <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
 <li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li>
       <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li>
@@ -179,7 +175,7 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
 </div>
 
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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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