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authorJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:35:15 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:35:15 +0100
commit0bd507131a9bb180afe6e843681330956086be9b (patch)
tree8117537d98c50ba29e61605e790984d494782de7 /vignettes/compiled_models.html
parent3151647526f299686b68420a83ae38cd7f3d08f5 (diff)
Vignettes rebuilt by staticdocs::build_site() for static documentation on r-forge
Diffstat (limited to 'vignettes/compiled_models.html')
-rw-r--r--vignettes/compiled_models.html47
1 files changed, 21 insertions, 26 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 3d92a7b8..92919da9 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -82,13 +82,8 @@ img {
<pre><code>## gcc
## &quot;/usr/bin/gcc&quot;</code></pre>
<p>First, we build a simple degradation model for a parent compound with one metabolite.</p>
-<pre class="r"><code>library(&quot;mkin&quot;)</code></pre>
-<pre><code>## Loading required package: minpack.lm
-## Loading required package: rootSolve
-## Loading required package: inline
-## Loading required package: methods
-## Loading required package: parallel</code></pre>
-<pre class="r"><code>SFO_SFO &lt;- mkinmod(
+<pre class="r"><code>library(&quot;mkin&quot;)
+SFO_SFO &lt;- mkinmod(
parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
m1 = mkinsub(&quot;SFO&quot;))</code></pre>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
@@ -104,19 +99,19 @@ smb.1 &lt;- summary(mb.1)[-1]
rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
print(smb.1)</code></pre>
<pre><code>## min lq mean median uq
-## deSolve, not compiled 4920.5498 4957.8305 5073.8005 4995.1112 5150.4259
-## Eigenvalue based 792.7603 820.6244 849.2773 848.4885 877.5358
-## deSolve, compiled 663.5431 673.4949 678.4844 683.4468 685.9551
+## deSolve, not compiled 9307.3194 9319.9546 9332.8171 9332.5899 9345.5659
+## Eigenvalue based 855.3608 855.8081 869.4725 856.2555 876.5283
+## deSolve, compiled 686.6143 687.9256 698.0279 689.2369 703.7346
## max neval cld
-## deSolve, not compiled 5305.7406 3 b
-## Eigenvalue based 906.5832 3 a
-## deSolve, compiled 688.4634 3 a</code></pre>
-<p>We see that using the compiled model is by a factor of 7.3 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>
+## deSolve, not compiled 9358.5420 3 c
+## Eigenvalue based 896.8012 3 b
+## deSolve, compiled 718.2324 3 a</code></pre>
+<p>We see that using the compiled model is by a factor of 13.5 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 class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
-<pre><code>## median
-## deSolve, not compiled 7.308706
-## Eigenvalue based 1.241484
-## deSolve, compiled 1.000000</code></pre>
+<pre><code>## median
+## deSolve, not compiled 13.540468
+## Eigenvalue based 1.242324
+## deSolve, compiled 1.000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
<h2>Benchmark for a model that can not be solved with Eigenvalues</h2>
@@ -133,17 +128,17 @@ smb.2 &lt;- summary(mb.2)[-1]
rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
print(smb.2)</code></pre>
<pre><code>## min lq mean median uq
-## deSolve, not compiled 10.710141 10.757988 10.810178 10.805835 10.860196
-## deSolve, compiled 1.200581 1.203966 1.211877 1.207351 1.217525
+## deSolve, not compiled 20.130709 20.147223 20.180429 20.163737 20.205289
+## deSolve, compiled 1.235864 1.255748 1.267458 1.275632 1.283255
## max neval cld
-## deSolve, not compiled 10.914558 3 b
-## deSolve, compiled 1.227699 3 a</code></pre>
+## deSolve, not compiled 20.246841 3 b
+## deSolve, compiled 1.290878 3 a</code></pre>
<pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
<pre><code>## median
-## deSolve, not compiled 8.950036
-## deSolve, compiled 1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code using the inline package!</p>
-<p>This vignette was built with mkin 0.9.40.900 on</p>
+## deSolve, not compiled 15.80686
+## deSolve, compiled 1.00000</code></pre>
+<p>Here we get a performance benefit of a factor of 15.8 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>This vignette was built with mkin 0.9.41 on</p>
<pre><code>## R version 3.2.2 (2015-08-14)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)</code></pre>

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