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diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index af04f755..d85246f8 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,10 +9,7 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -80,7 +77,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -155,8 +152,8 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:17:55 2018 -## Date of summary: Thu Mar 1 14:17:55 2018 +## Date of fit: Fri Mar 9 23:09:48 2018 +## Date of summary: Fri Mar 9 23:09:48 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -164,7 +161,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.993 s +## Fitted with method Port using 153 model solutions performed in 0.99 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex b4fa2ff4..c0fab72d 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex ba06ce31..47916477 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 5de06ad5..196a0c4f 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -9,10 +9,7 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> -<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -80,7 +77,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -103,15 +100,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:31:57 2018 -## Date of summary: Thu Mar 1 14:31:57 2018 +## Date of fit: Fri Mar 9 23:09:50 2018 +## Date of summary: Fri Mar 9 23:09:50 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.24 s +## Fitted with method Port using 37 model solutions performed in 0.264 s ## ## Weighting: none ## @@ -194,15 +191,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:31:59 2018 -## Date of summary: Thu Mar 1 14:32:00 2018 +## Date of fit: Fri Mar 9 23:09:52 2018 +## Date of summary: Fri Mar 9 23:09:52 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.375 s +## Fitted with method Port using 611 model solutions performed in 1.451 s ## ## Weighting: none ## @@ -289,15 +286,15 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:00 2018 -## Date of summary: Thu Mar 1 14:32:00 2018 +## Date of fit: Fri Mar 9 23:09:53 2018 +## Date of summary: Fri Mar 9 23:09:53 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.158 s +## Fitted with method Port using 81 model solutions performed in 0.175 s ## ## Weighting: none ## @@ -360,8 +357,8 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:01 2018 -## Date of summary: Thu Mar 1 14:32:01 2018 +## Date of fit: Fri Mar 9 23:09:54 2018 +## Date of summary: Fri Mar 9 23:09:54 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -370,7 +367,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.708 s +## Fitted with method Port using 336 model solutions performed in 0.739 s ## ## Weighting: none ## @@ -452,8 +449,8 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:02 2018 -## Date of summary: Thu Mar 1 14:32:02 2018 +## Date of fit: Fri Mar 9 23:09:55 2018 +## Date of summary: Fri Mar 9 23:09:55 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -462,7 +459,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.287 s +## Fitted with method Port using 137 model solutions performed in 0.293 s ## ## Weighting: none ## @@ -553,15 +550,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:03 2018 -## Date of summary: Thu Mar 1 14:32:03 2018 +## Date of fit: Fri Mar 9 23:09:55 2018 +## Date of summary: Fri Mar 9 23:09:56 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.089 s +## Fitted with method Port using 46 model solutions performed in 0.09 s ## ## Weighting: none ## @@ -613,8 +610,8 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Thu Mar 1 14:32:03 2018 -## Date of summary: Thu Mar 1 14:32:03 2018 +## Date of fit: Fri Mar 9 23:09:56 2018 +## Date of summary: Fri Mar 9 23:09:56 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 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src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -80,7 +77,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> @@ -101,7 +98,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) { - b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw">benchmark</span>( + b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>( <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), @@ -117,10 +114,15 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, -## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> -<pre><code>## [1] "R package benchmark is not available"</code></pre> -<p>We see that using the compiled model is by a factor of around NA 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><code>## test replications elapsed relative user.self sys.self +## 3 deSolve, compiled 3 2.044 1.000 2.042 0 +## 1 deSolve, not compiled 3 14.198 6.946 14.185 0 +## 2 Eigenvalue based 3 2.751 1.346 2.747 0 +## user.child sys.child +## 3 0 0 +## 1 0 0 +## 2 0 0</code></pre> +<p>We see that using the compiled model is by a factor of around 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> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> @@ -131,7 +133,7 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>)) - b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw">benchmark</span>( + b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>( <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>), @@ -142,11 +144,14 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>) }</code></pre></div> -<pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## Warning in library(package, lib.loc = lib.loc, character.only = TRUE, -## logical.return = TRUE, : es gibt kein Paket namens 'rbenchmark'</code></pre> -<pre><code>## [1] "R package benchmark is not available"</code></pre> -<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<pre><code>## test replications elapsed relative user.self sys.self +## 2 deSolve, compiled 3 3.695 1.000 3.692 0 +## 1 deSolve, not compiled 3 31.143 8.428 31.114 0 +## user.child sys.child +## 2 0 0 +## 1 0 0</code></pre> +<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/articles/index.html b/docs/articles/index.html index 2b16580a..c0c5864b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ 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<h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-01</h4> + <h4 class="date">2018-03-09</h4> </div> |
