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authorJohannes Ranke <jranke@uni-bremen.de>2016-11-03 14:33:05 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-11-03 17:48:31 +0100
commitf39815aa87272849f8e0c808099c4cee780c2a81 (patch)
treed3f59ae226591252e17737e12bae7f90be278b7b /docs/articles/compiled_models.html
parentbad0c7caff62aa90225ae8acee43b297bdc28b25 (diff)
Static documentation rebuilt by pkgdown::build_site()
Using pkgdown with PR hadley/pkgdown#212
Diffstat (limited to 'docs/articles/compiled_models.html')
-rw-r--r--docs/articles/compiled_models.html43
1 files changed, 23 insertions, 20 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index e02b9cf3..5a04168e 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -16,13 +16,16 @@
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../index.html">Home</a>
+ <a href="../reference/index.html">Reference</a>
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- <a href="../reference/index.html">Reference</a>
+ <a href="../articles/index.html">Articles</a>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
- <a href="https://github.com/jranke/mkin">
+ <a href="http://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
</a>
@@ -38,7 +41,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2016-10-26</h4>
+ <h4 class="date">2016-11-03</h4>
</div>
@@ -75,21 +78,21 @@ mb<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw">micr
<span class="kw">print</span>(mb<span class="fl">.1</span>)</code></pre></div>
<pre><code>## Unit: milliseconds
## expr min lq mean median uq
-## deSolve, not compiled 6298.7342 6308.6792 6343.9668 6318.6243 6366.5831
-## Eigenvalue based 871.7379 880.7757 903.5267 889.8135 919.4211
-## deSolve, compiled 724.9025 730.6729 732.9837 736.4432 737.0243
+## deSolve, not compiled 6306.4527 6340.7895 6403.5937 6375.1264 6452.1643
+## Eigenvalue based 918.0808 929.7217 948.9742 941.3626 964.4210
+## deSolve, compiled 736.1337 753.6016 773.5605 771.0696 792.2739
## max neval cld
-## 6414.5420 3 c
-## 949.0287 3 b
-## 737.6054 3 a</code></pre>
+## 6529.2022 3 b
+## 987.4793 3 a
+## 813.4783 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.1</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_SFO_SFO-1.png" width="672"></p>
-<p>We see that using the compiled model is by a factor of 8.6 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>
+<p>We see that using the compiled model is by a factor of 8.3 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>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">rownames</span>(smb<span class="fl">.1</span>) &lt;-<span class="st"> </span>smb<span class="fl">.1</span>$expr
smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="fl">.1</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
-## deSolve, not compiled 8.579920
-## Eigenvalue based 1.208258
+## deSolve, not compiled 8.267900
+## Eigenvalue based 1.220853
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -111,20 +114,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<span class="kw">print</span>(mb<span class="fl">.2</span>)</code></pre></div>
<pre><code>## Unit: seconds
## expr min lq mean median uq
-## deSolve, not compiled 13.265212 13.330161 13.412053 13.395109 13.485473
-## deSolve, compiled 1.322466 1.326851 1.364827 1.331236 1.386007
+## deSolve, not compiled 13.604720 13.667244 13.689764 13.729768 13.732286
+## deSolve, compiled 1.305077 1.311124 1.328943 1.317172 1.340876
## max neval cld
-## 13.575837 3 b
-## 1.440779 3 a</code></pre>
+## 13.734804 3 b
+## 1.364579 3 a</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span>[<span class="st">"median"</span>]/smb<span class="fl">.2</span>[<span class="st">"deSolve, compiled"</span>, <span class="st">"median"</span>]</code></pre></div>
<pre><code>## median
## 1 NA
## 2 NA</code></pre>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">autoplot</span>(mb<span class="fl">.2</span>)</code></pre></div>
<p><img src="compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png" width="672"></p>
-<p>Here we get a performance benefit of a factor of 10.1 using the version of the differential equation model compiled from C code!</p>
+<p>Here we get a performance benefit of a factor of 10.4 using the version of the differential equation model compiled from C code!</p>
<p>This vignette was built with mkin 0.9.44.9000 on</p>
-<pre><code>## R version 3.3.1 (2016-06-21)
+<pre><code>## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)</code></pre>
<pre><code>## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre>
@@ -144,7 +147,7 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class="
<footer><div class="copyright">
- <p>Developed by Johannes Ranke, Eurofins Regulatory AG.</p>
+ <p>Developed by Johannes Ranke.</p>
</div>
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