Static documentation rebuilt by pkgdown

1 files changed, 45 insertions, 45 deletions

diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 183c9658..17387187 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -84,7 +84,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-07-18</h4>
+            <h4 class="date">2018-09-06</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -97,37 +97,37 @@
 <h2 class="hasAnchor">
 <a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2>
 <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</a></code></pre></div>
 <pre><code>##            gcc 
 ## "/usr/bin/gcc"</code></pre>
 <p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)
-SFO_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">"SFO"</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>))</code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
+<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb3-3" data-line-number="3">  <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a>
+<a class="sourceLine" id="cb3-4" data-line-number="4">  <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></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"><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"><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>),
-    <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_<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>])
-} <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>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb5-2" data-line-number="2">  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>(</a>
+<a class="sourceLine" id="cb5-3" data-line-number="3">    <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,</a>
+<a class="sourceLine" id="cb5-4" data-line-number="4">                                      <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a>
+<a class="sourceLine" id="cb5-5" data-line-number="5">                                      <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-6" data-line-number="6">    <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,</a>
+<a class="sourceLine" id="cb5-7" data-line-number="7">                                 <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-8" data-line-number="8">    <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,</a>
+<a class="sourceLine" id="cb5-9" data-line-number="9">                                  <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb5-10" data-line-number="10">    <span class="dt">replications =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb5-11" data-line-number="11">  <span class="kw">print</span>(b<span class="fl">.1</span>)</a>
+<a class="sourceLine" id="cb5-12" data-line-number="12">  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>])</a>
+<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a>
+<a class="sourceLine" id="cb5-14" data-line-number="14">  factor_SFO_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb5-15" data-line-number="15">  <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></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   2.044    1.000     2.043        0
-## 1 deSolve, not compiled            3  16.571    8.107    16.565        0
-## 2      Eigenvalue based            3   2.499    1.223     2.496        0
+## 3     deSolve, compiled            3   2.112    1.000     2.110        0
+## 1 deSolve, not compiled            3  16.633    7.875    16.624        0
+## 2      Eigenvalue based            3   2.637    1.249     2.635        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -138,31 +138,31 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mki
 <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"><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"><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>),
-    <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>])
-} <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>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a>
+<a class="sourceLine" id="cb8-2" data-line-number="2">  FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb8-3" data-line-number="3">    <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>),</a>
+<a class="sourceLine" id="cb8-4" data-line-number="4">    <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a>
+<a class="sourceLine" id="cb8-5" data-line-number="5"></a>
+<a class="sourceLine" id="cb8-6" data-line-number="6">  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>(</a>
+<a class="sourceLine" id="cb8-7" data-line-number="7">    <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,</a>
+<a class="sourceLine" id="cb8-8" data-line-number="8">                                      <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a>
+<a class="sourceLine" id="cb8-9" data-line-number="9">    <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>),</a>
+<a class="sourceLine" id="cb8-10" data-line-number="10">    <span class="dt">replications =</span> <span class="dv">3</span>)</a>
+<a class="sourceLine" id="cb8-11" data-line-number="11">  <span class="kw">print</span>(b<span class="fl">.2</span>)</a>
+<a class="sourceLine" id="cb8-12" data-line-number="12">  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>])</a>
+<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a>
+<a class="sourceLine" id="cb8-14" data-line-number="14">  factor_FOMC_SFO &lt;-<span class="st"> </span><span class="ot">NA</span></a>
+<a class="sourceLine" id="cb8-15" data-line-number="15">  <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a>
+<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></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   3.592    1.000     3.589        0
-## 1 deSolve, not compiled            3  35.340    9.839    35.324        0
+## 2     deSolve, compiled            3   3.720    1.000     3.718        0
+## 1 deSolve, not compiled            3  34.677    9.322    34.661        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>
-<p>Here we get a performance benefit of a factor of 10 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>
+<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p>
+<p>This vignette was built with mkin 0.9.47.2 on</p>
 <pre><code>## R version 3.5.1 (2018-07-02)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)</code></pre>