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authorJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2018-03-09 23:14:39 +0100
commit0b677308e3ffbf742880f05cc54da469f3ecc854 (patch)
tree26dab561d6f5a31923b28b5fdf6c1859727dfe7f /vignettes/compiled_models.html
parent5aec8e34680e05671347f7577ae36c9ad8e37063 (diff)
Another rebuild of the static docs
Now with rbenchmark installed, to get results for the compiled_models vignette
Diffstat (limited to 'vignettes/compiled_models.html')
-rw-r--r--vignettes/compiled_models.html38
1 files changed, 19 insertions, 19 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 8aaa70d6..d8c5b19b 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -12,7 +12,7 @@
<meta name="author" content="Johannes Ranke" />
-<meta name="date" content="2018-01-14" />
+<meta name="date" content="2018-03-09" />
<title>Performance benefit by using compiled model definitions in mkin</title>
@@ -70,7 +70,7 @@ code > span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Inf
<h1 class="title toc-ignore">Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author"><em>Johannes Ranke</em></h4>
-<h4 class="date"><em>2018-01-14</em></h4>
+<h4 class="date"><em>2018-03-09</em></h4>
@@ -87,27 +87,27 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
<span class="dt">m1 =</span> <span class="kw">mkinsub</span>(<span class="st">&quot;SFO&quot;</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">&quot;deSolve, not compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">&quot;deSolve, not compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,
<span class="dt">solution_type =</span> <span class="st">&quot;deSolve&quot;</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">&quot;Eigenvalue based&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">&quot;Eigenvalue based&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,
<span class="dt">solution_type =</span> <span class="st">&quot;eigen&quot;</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
- <span class="st">&quot;deSolve, compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_2006_D,
+ <span class="st">&quot;deSolve, compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,
<span class="dt">solution_type =</span> <span class="st">&quot;deSolve&quot;</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">&quot;1&quot;</span>, <span class="st">&quot;relative&quot;</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">&quot;R package benchmark is not available&quot;</span>)
}</code></pre></div>
<pre><code>## Loading required package: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.005 1.000 2.000 0.004
-## 1 deSolve, not compiled 3 14.202 7.083 14.196 0.000
-## 2 Eigenvalue based 3 2.427 1.210 2.428 0.000
+## 3 deSolve, compiled 3 1.980 1.000 1.979 0
+## 1 deSolve, not compiled 3 13.926 7.033 13.914 0
+## 2 Eigenvalue based 3 2.362 1.193 2.360 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -117,35 +117,35 @@ SFO_SFO &lt;-<span class="st"> </span><span class="kw">mkinmod</span>(
<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2>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">mkinmod</span>(
<span class="dt">parent =</span> <span class="kw">mkinsub</span>(<span class="st">&quot;FOMC&quot;</span>, <span class="st">&quot;m1&quot;</span>),
<span class="dt">m1 =</span> <span class="kw">mkinsub</span>( <span class="st">&quot;SFO&quot;</span>))
b<span class="fl">.2</span> &lt;-<span class="st"> </span><span class="kw">benchmark</span>(
- <span class="st">&quot;deSolve, not compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_2006_D,
+ <span class="st">&quot;deSolve, not compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</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">&quot;deSolve, compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</span>(FOMC_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),
+ <span class="st">&quot;deSolve, compiled&quot;</span> =<span class="st"> </span><span class="kw">mkinfit</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">&quot;1&quot;</span>, <span class="st">&quot;relative&quot;</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">&quot;R package benchmark is not available&quot;</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 3.489 1.000 3.488 0
-## 1 deSolve, not compiled 3 28.906 8.285 28.904 0
+## 2 deSolve, compiled 3 3.437 1.000 3.433 0
+## 1 deSolve, not compiled 3 30.406 8.847 30.380 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>
+<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 0.9.46.3 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>

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