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authorJohannes Ranke <jranke@uni-bremen.de>2015-06-26 16:08:04 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-26 16:08:04 +0200
commitcc0d7a44cccac46ea1c71cf663aadee0efb2bba7 (patch)
tree146d1cbcb29ce4831f9ff013bf03a8637b348e8f /vignettes/compiled_models.html
parent4cc13bcd8305611cb730faecae3511acf7c92043 (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.html39
1 files changed, 17 insertions, 22 deletions
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 12454559..a62f3826 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>
@@ -104,18 +99,18 @@ 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 5292.0165 5313.7620 5364.5733 5335.5075 5400.8517
-## Eigenvalue based 893.9459 921.1984 936.1750 948.4509 957.2895
-## deSolve, compiled 742.7723 745.4243 750.1963 748.0763 753.9083
+## deSolve, not compiled 7047.6039 7083.3201 7123.5962 7119.0364 7161.5924
+## Eigenvalue based 901.5593 924.3357 968.8689 947.1121 1002.5238
+## deSolve, compiled 765.7604 770.7657 786.8638 775.7709 797.4156
## max neval
-## deSolve, not compiled 5466.1959 3
-## Eigenvalue based 966.1282 3
-## deSolve, compiled 759.7404 3</code></pre>
-<p>We see that using the compiled model is by a factor of 7.1 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 7204.1483 3
+## Eigenvalue based 1057.9355 3
+## deSolve, compiled 819.0602 3</code></pre>
+<p>We see that using the compiled model is by a factor of 9.2 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 7.132304
-## Eigenvalue based 1.267853
+## deSolve, not compiled 9.176725
+## Eigenvalue based 1.220866
## deSolve, compiled 1.000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -133,16 +128,16 @@ 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 11.277340 11.336373 11.392883 11.395407 11.450654
-## deSolve, compiled 1.339204 1.342662 1.350783 1.346121 1.356573
+## deSolve, not compiled 14.080456 14.209689 14.287313 14.338922 14.390742
+## deSolve, compiled 1.467266 1.521451 1.555168 1.575636 1.599119
## max neval
-## deSolve, not compiled 11.505901 3
-## deSolve, compiled 1.367025 3</code></pre>
+## deSolve, not compiled 14.442561 3
+## deSolve, compiled 1.622601 3</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 8.465368
+## deSolve, not compiled 9.100402
## deSolve, compiled 1.000000</code></pre>
-<p>Here we get a performance benefit of a factor of 8.5 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>Here we get a performance benefit of a factor of 9.1 using the version of the differential equation model compiled from C code using the inline package!</p>
<p>This vignette was built with mkin 0.9.39 on</p>
<pre><code>## R version 3.2.1 (2015-06-18)
## Platform: x86_64-pc-linux-gnu (64-bit)

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