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Diffstat (limited to 'docs/articles')
88 files changed, 74 insertions, 58 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index f32d7f82..1c4edbd0 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -24,7 +24,13 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -110,8 +116,8 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.44.9000 ## R version: 3.3.2 -## Date of fit: Wed Nov 2 16:25:22 2016 -## Date of summary: Wed Nov 2 16:25:22 2016 +## Date of fit: Fri Nov 4 16:56:20 2016 +## Date of summary: Fri Nov 4 16:56:20 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -119,7 +125,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.665 s +## Fitted with method Port using 153 model solutions performed in 0.661 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData Binary files differindex 969644fa..f670208c 100644 --- a/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData +++ b/docs/articles/FOCUS_D_cache/html/data_df09328a15a9c09625fe6f7d481671d8.RData diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData Binary files differindex 17db087e..9a067af3 100644 --- a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData +++ 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c0b0c2db..00000000 --- a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png Binary files differdeleted file mode 100644 index 6700e527..00000000 --- a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-6-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6a9c6ba5..2244a359 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -24,7 +24,13 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> @@ -57,15 +63,15 @@ 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: Fri Nov 4 15:38:03 2016 -## Date of summary: Fri Nov 4 15:38:03 2016 +## Date of fit: Fri Nov 4 16:56:21 2016 +## Date of summary: Fri Nov 4 16:56:21 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.089 s +## Fitted with method Port using 37 model solutions performed in 0.087 s ## ## Weighting: none ## @@ -150,8 +156,8 @@ 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: Fri Nov 4 15:38:04 2016 -## Date of summary: Fri Nov 4 15:38:04 2016 +## Date of fit: Fri Nov 4 16:56:21 2016 +## Date of summary: Fri Nov 4 16:56:21 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -163,7 +169,7 @@ 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 0.446 s +## Fitted with method Port using 188 model solutions performed in 0.46 s ## ## Weighting: none ## @@ -247,15 +253,15 @@ 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: Fri Nov 4 15:38:05 2016 -## Date of summary: Fri Nov 4 15:38:05 2016 +## Date of fit: Fri Nov 4 16:56:22 2016 +## Date of summary: Fri Nov 4 16:56:22 2016 ## ## Equations: ## d_parent = - (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 0.199 s ## ## Weighting: none ## @@ -317,8 +323,8 @@ 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: Fri Nov 4 15:38:06 2016 -## Date of summary: Fri Nov 4 15:38:06 2016 +## Date of fit: Fri Nov 4 16:56:23 2016 +## Date of summary: Fri Nov 4 16:56:23 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -327,7 +333,7 @@ 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 0.815 s +## Fitted with method Port using 336 model solutions performed in 0.81 s ## ## Weighting: none ## @@ -406,8 +412,8 @@ 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: Fri Nov 4 15:38:07 2016 -## Date of summary: Fri Nov 4 15:38:07 2016 +## Date of fit: Fri Nov 4 16:56:24 2016 +## Date of summary: Fri Nov 4 16:56:25 2016 ## ## Equations: ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -416,7 +422,7 @@ 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 0.339 s +## Fitted with method Port using 137 model solutions performed in 0.335 s ## ## Weighting: none ## @@ -506,15 +512,15 @@ 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: Fri Nov 4 15:38:07 2016 -## Date of summary: Fri Nov 4 15:38:08 2016 +## Date of fit: Fri Nov 4 16:56:25 2016 +## Date of summary: Fri Nov 4 16:56:25 2016 ## ## Equations: ## d_parent = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.112 s +## Fitted with method Port using 46 model solutions performed in 0.109 s ## ## Weighting: none ## @@ -566,15 +572,15 @@ 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: Fri Nov 4 15:38:08 2016 -## Date of summary: Fri Nov 4 15:38:08 2016 +## Date of fit: Fri Nov 4 16:56:25 2016 +## Date of summary: Fri Nov 4 16:56:25 2016 ## ## Equations: ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.148 s +## Fitted with method Port 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class="fl">.1</span>)</code></pre></div> <pre><code>## Unit: milliseconds ## expr min lq mean median uq -## deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726 -## Eigenvalue based 880.1617 890.3517 911.2758 900.5416 926.8328 -## deSolve, compiled 739.4343 749.6078 753.6543 759.7813 760.7643 +## deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069 +## Eigenvalue based 925.7797 935.9924 939.8725 946.2051 946.9189 +## deSolve, compiled 740.2821 750.0017 767.8440 759.7212 781.6249 ## max neval cld -## 6692.5522 3 c -## 953.1240 3 b -## 761.7474 3 a</code></pre> +## 6671.1797 3 b +## 947.6327 3 a +## 803.5287 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 8.5 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 8.708286 -## Eigenvalue based 1.185264 +## deSolve, not compiled 8.464993 +## Eigenvalue based 1.245464 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -108,18 +114,18 @@ 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 13.756286 13.813205 13.874083 13.870125 13.932982 -## deSolve, compiled 1.323196 1.372916 1.391915 1.422635 1.426274 +## deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741 +## deSolve, compiled 1.316871 1.322577 1.358847 1.328283 1.379834 ## max neval cld -## 13.995838 3 b -## 1.429913 3 a</code></pre> +## 13.954275 3 b +## 1.431386 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 9.7 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 10.5 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 51846e6c..57730131 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 f6e4cb08..50adff32 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 9f7cdd74..cd6a7bea 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,12 @@ </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 5f6ae46c..8a24352c 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -24,7 +24,13 @@ <li> <a href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse --> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="http://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index 03ece635..c8b1e877 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,13 +1,8 @@ base -datasets -utils -grDevices -graphics -stats knitr minpack.lm rootSolve -methods inline -parallel mkin +microbenchmark +ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData 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