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Diffstat (limited to 'docs/articles/compiled_models.html')
| -rw-r--r-- | docs/articles/compiled_models.html | 33 |
1 files changed, 18 insertions, 15 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 2850a9ae..660af1d1 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -37,6 +37,9 @@ <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> </ul></li> +<li> + <a href="../news/index.html">News</a> +</li> </ul><ul class="nav navbar-nav navbar-right"><li> <a href="http://github.com/jranke/mkin"> <span class="fa fa-github fa-lg"></span> @@ -96,21 +99,21 @@ 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 4973.8901 4975.2320 5000.4065 4976.5739 5013.6648 -## Eigenvalue based 848.4335 859.7111 886.9766 870.9887 906.2481 -## deSolve, compiled 702.8916 705.1930 706.2696 707.4944 707.9587 +## deSolve, not compiled 5006.3815 5014.4629 5112.7115 5022.5443 5165.8765 +## Eigenvalue based 840.3027 874.3549 892.0593 908.4071 917.9376 +## deSolve, compiled 706.9909 712.8031 723.4380 718.6154 731.6615 ## max neval cld -## 5050.7556 3 c -## 941.5075 3 b -## 708.4229 3 a</code></pre> +## 5309.2087 3 b +## 927.4680 3 a +## 744.7077 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 7 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 7.034082 -## Eigenvalue based 1.231089 +## deSolve, not compiled 6.989197 +## Eigenvalue based 1.264108 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -131,20 +134,20 @@ smb<span class="fl">.1</span>[<span class="st">"median"</span>]/smb<span class=" <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">smb<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">summary</span>(mb<span class="fl">.2</span>) <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 10.819486 10.846433 10.863732 10.873381 10.885855 -## deSolve, compiled 1.300192 1.301168 1.304769 1.302144 1.307058 +## expr min lq mean median uq +## deSolve, not compiled 11.015990 11.17783 11.24827 11.339674 11.364403 +## deSolve, compiled 1.285264 1.29794 1.32988 1.310616 1.352189 ## max neval cld -## 10.898330 3 b -## 1.311972 3 a</code></pre> +## 11.389132 3 b +## 1.393762 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 8.4 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> +<p>Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.45 on</p> <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> |