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Diffstat (limited to 'docs/articles/compiled_models.html')
| -rw-r--r-- | docs/articles/compiled_models.html | 28 |
1 files changed, 14 insertions, 14 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 1446a357..ce149bc5 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -41,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> @@ -78,21 +78,21 @@ mb<span class="fl">.1</span> <-<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 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524 -## Eigenvalue based 858.2035 903.1770 926.2132 948.1505 960.2181 -## deSolve, compiled 721.0067 739.1361 745.9964 757.2656 758.4913 +## deSolve, not compiled 6341.1795 6363.5977 6373.7748 6386.0158 6390.0724 +## Eigenvalue based 907.1699 908.8498 921.8335 910.5297 929.1653 +## deSolve, compiled 747.5311 752.3718 754.2086 757.2125 757.5474 ## max neval cld -## 6364.0611 3 c -## 972.2856 3 b -## 759.7171 3 a</code></pre> +## 6394.1290 3 c +## 947.8008 3 b +## 757.8823 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 8.4 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>) <-<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 8.360665 -## Eigenvalue based 1.252071 +## deSolve, not compiled 8.433585 +## Eigenvalue based 1.202476 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -114,11 +114,11 @@ 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 13.601046 13.602861 13.619563 13.604676 13.628821 -## deSolve, compiled 1.341581 1.346263 1.348298 1.350944 1.351657 -## max neval cld -## 13.65297 3 b -## 1.35237 3 a</code></pre> +## deSolve, not compiled 13.214250 13.248908 13.384577 13.283565 13.469740 +## deSolve, compiled 1.303868 1.307484 1.332879 1.311099 1.347384 +## max neval cld +## 13.655915 3 b +## 1.383669 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 |