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Diffstat (limited to 'docs/articles/compiled_models.html')
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1 files changed, 35 insertions, 22 deletions
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index ce149bc5..31340867 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -16,14 +16,27 @@ </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> -<li> - <a href="../articles/index.html">Articles</a> -</li> -<li> - <a href="../news/index.html">News</a> + <a href="../reference/index.html">Function reference</a> </li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"><li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + </ul></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> @@ -78,21 +91,21 @@ 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 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 +## deSolve, not compiled 6559.0772 6574.0500 6642.0659 6589.0229 6683.5603 +## Eigenvalue based 921.0723 931.1284 940.3973 941.1845 950.0598 +## deSolve, compiled 736.6534 741.6706 756.3600 746.6878 766.2132 ## max neval cld -## 6394.1290 3 c -## 947.8008 3 b -## 757.8823 3 a</code></pre> +## 6778.0978 3 c +## 958.9351 3 b +## 785.7386 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> +<p>We see that using the compiled model is by a factor of 8.8 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 8.433585 -## Eigenvalue based 1.202476 +## deSolve, not compiled 8.824334 +## Eigenvalue based 1.260479 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -113,19 +126,19 @@ 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 13.214250 13.248908 13.384577 13.283565 13.469740 -## deSolve, compiled 1.303868 1.307484 1.332879 1.311099 1.347384 +## expr min lq mean median uq +## deSolve, not compiled 13.587184 13.616178 13.673277 13.64517 13.716324 +## deSolve, compiled 1.307508 1.317114 1.337594 1.32672 1.352637 ## max neval cld -## 13.655915 3 b -## 1.383669 3 a</code></pre> +## 13.787476 3 b +## 1.378553 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 10.3 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 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) |