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Diffstat (limited to 'docs/articles')
| -rw-r--r-- | docs/articles/FOCUS_L.html | 42 | ||||
| -rw-r--r-- | docs/articles/compiled_models.html | 37 | ||||
| -rw-r--r-- | docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png | bin | 9742 -> 9519 bytes | |||
| -rw-r--r-- | docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png | bin | 10742 -> 10832 bytes | |||
| -rw-r--r-- | docs/articles/index.html | 2 |
5 files changed, 43 insertions, 38 deletions
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6a25282b..feceab6f 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -76,15 +76,15 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:15 2016 -## Date of summary: Thu Dec 8 07:59:15 2016 +## Date of fit: Thu Dec 8 08:18:47 2016 +## Date of summary: Thu Dec 8 08:18:47 2016 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.087 s +## Fitted with method Port using 37 model solutions performed in 0.084 s ## ## Weighting: none ## @@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:15 2016 -## Date of summary: Thu Dec 8 07:59:15 2016 +## Date of fit: Thu Dec 8 08:18:47 2016 +## Date of summary: Thu Dec 8 08:18:47 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 188 model solutions performed in 0.436 s +## Fitted with method Port using 188 model solutions performed in 0.462 s ## ## Weighting: none ## @@ -266,15 +266,15 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:16 2016 -## Date of summary: Thu Dec 8 07:59:16 2016 +## Date of fit: Thu Dec 8 08:18:48 2016 +## Date of summary: Thu Dec 8 08:18:48 2016 ## ## 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 0.19 s +## Fitted with method Port using 81 model solutions performed in 0.201 s ## ## Weighting: none ## @@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re <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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:17 2016 -## Date of summary: Thu Dec 8 07:59:17 2016 +## Date of fit: Thu Dec 8 08:18:49 2016 +## Date of summary: Thu Dec 8 08:18:49 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../re ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.785 s +## Fitted with method Port using 336 model solutions performed in 0.767 s ## ## Weighting: none ## @@ -425,8 +425,8 @@ 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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:18 2016 -## Date of summary: Thu Dec 8 07:59:18 2016 +## Date of fit: Thu Dec 8 08:18:50 2016 +## Date of summary: Thu Dec 8 08:18:51 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -435,7 +435,7 @@ 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 0.319 s +## Fitted with method Port using 137 model solutions performed in 0.311 s ## ## Weighting: none ## @@ -525,15 +525,15 @@ 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: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:19 2016 -## Date of summary: Thu Dec 8 07:59:19 2016 +## Date of fit: Thu Dec 8 08:18:51 2016 +## Date of summary: Thu Dec 8 08:18:51 2016 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.107 s +## Fitted with method Port using 46 model solutions performed in 0.118 s ## ## Weighting: none ## @@ -585,15 +585,15 @@ 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">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Thu Dec 8 07:59:19 2016 -## Date of summary: Thu Dec 8 07:59:19 2016 +## Date of fit: Thu Dec 8 08:18:51 2016 +## Date of summary: Thu Dec 8 08:18:51 2016 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.152 s +## Fitted with method Port using 66 model solutions performed in 0.151 s ## ## Weighting: none ## diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index d39caf12..2850a9ae 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -67,8 +67,13 @@ <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>) -SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>)</code></pre></div> +<pre><code>## Loading required package: minpack.lm</code></pre> +<pre><code>## Loading required package: rootSolve</code></pre> +<pre><code>## Loading required package: inline</code></pre> +<pre><code>## Loading required package: methods</code></pre> +<pre><code>## Loading required package: parallel</code></pre> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>( <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</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>))</code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> @@ -91,21 +96,21 @@ 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 6263.2932 6273.5107 6286.8574 6283.7283 6298.6394 -## Eigenvalue based 865.5257 872.4146 892.2705 879.3036 905.6429 -## deSolve, compiled 716.7534 717.9075 724.6869 719.0617 728.6537 +## 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 ## max neval cld -## 6313.5506 3 c -## 931.9821 3 b -## 738.2457 3 a</code></pre> +## 5050.7556 3 c +## 941.5075 3 b +## 708.4229 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 8.7 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> +<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 8.738789 -## Eigenvalue based 1.222849 +## deSolve, not compiled 7.034082 +## Eigenvalue based 1.231089 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -127,18 +132,18 @@ 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 13.487097 13.492149 13.528060 13.497201 13.548541 -## deSolve, compiled 1.307845 1.318979 1.322967 1.330114 1.330528 +## 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 ## max neval cld -## 13.599881 3 b -## 1.330941 3 a</code></pre> +## 10.898330 3 b +## 1.311972 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 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> <pre><code>## R version 3.3.2 (2016-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png Binary files differindex d881a0a2..c30550c9 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_FOMC_SFO-1.png diff --git a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png Binary files differindex b3faa16f..5f95613a 100644 --- a/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png +++ b/docs/articles/compiled_models_files/figure-html/benchmark_SFO_SFO-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index de5643c2..20792ba1 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -90,7 +90,7 @@ </header> <div class="page-header"> - <h1>Vignette reference <small>version 0.9.44.9000</small></h1> + <h1>Vignette reference <small>version 0.9.45</small></h1> </div> <div class="row"> |
