diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:01:53 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:22:42 +0100 |
| commit | c6086d1dd97ad2d6420625de7b8009b1b0f85d06 (patch) | |
| tree | 1a38fd690c94a556555ec71edff443bcfe609b7b /docs/articles | |
| parent | 9a8dfa8bd52664929fd4197f3e9c4e65b62cad53 (diff) | |
Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)
Using branch 'jranke' on jranke/pkgdown, fixing issues
hadley/pgkdown#178 and hadley/pkgdown#213
Remove plot=TRUE from mkinfit calls also in dontrun sections of examples
to avoid a flood png files documenting the progress of the fit.
Diffstat (limited to 'docs/articles')
20 files changed, 38 insertions, 42 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 776e1093..0ce7bd07 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -41,7 +41,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> diff --git a/docs/articles/FOCUS_D_cache/html/__packages b/docs/articles/FOCUS_D_cache/html/__packages index f8bbf624..c3c384b1 100644 --- a/docs/articles/FOCUS_D_cache/html/__packages +++ b/docs/articles/FOCUS_D_cache/html/__packages @@ -8,5 +8,3 @@ inline mkin rmarkdown knitr -microbenchmark -ggplot2 diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData Binary files differnew file mode 100644 index 00000000..36a4095f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_2_a17fdb1fd55c48e44fecf3303fab9127.rdx diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData Binary files differnew file mode 100644 index 00000000..b0731d7b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdb diff --git a/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx Binary files differnew file mode 100644 index 00000000..20f10d9f --- /dev/null +++ b/docs/articles/FOCUS_D_cache/html/plot_7ea6a8e7d5684cd6a8daf57a478ef419.rdx 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 fc237898..e44c1374 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 b0a7c26b..c7df3486 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 e7ec5308..c3009e4d 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -41,7 +41,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> @@ -63,15 +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: Thu Nov 17 22:58:18 2016 -## Date of summary: Thu Nov 17 22:58:18 2016 +## Date of fit: Fri Nov 18 15:22:03 2016 +## Date of summary: Fri Nov 18 15:22:03 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 0.103 s +## Fitted with method Port using 37 model solutions performed in 0.09 s ## ## Weighting: none ## @@ -156,8 +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: Thu Nov 17 22:58:19 2016 -## Date of summary: Thu Nov 17 22:58:19 2016 +## Date of fit: Fri Nov 18 15:22:04 2016 +## Date of summary: Fri Nov 18 15:22:04 2016 ## ## ## Warning: Optimisation by method Port did not converge. @@ -169,7 +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 0.462 s +## Fitted with method Port using 188 model solutions performed in 0.445 s ## ## Weighting: none ## @@ -253,15 +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: Thu Nov 17 22:58:20 2016 -## Date of summary: Thu Nov 17 22:58:20 2016 +## Date of fit: Fri Nov 18 15:22:05 2016 +## Date of summary: Fri Nov 18 15:22:05 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 0.195 s +## Fitted with method Port using 81 model solutions performed in 0.19 s ## ## Weighting: none ## @@ -323,8 +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: Thu Nov 17 22:58:21 2016 -## Date of summary: Thu Nov 17 22:58:21 2016 +## Date of fit: Fri Nov 18 15:22:06 2016 +## Date of summary: Fri Nov 18 15:22:06 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -333,7 +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 0.882 s +## Fitted with method Port using 336 model solutions performed in 0.803 s ## ## Weighting: none ## @@ -412,8 +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: Thu Nov 17 22:58:22 2016 -## Date of summary: Thu Nov 17 22:58:22 2016 +## Date of fit: Fri Nov 18 15:22:07 2016 +## Date of summary: Fri Nov 18 15:22:07 2016 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -422,7 +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 0.338 s +## Fitted with method Port using 137 model solutions performed in 0.329 s ## ## Weighting: none ## @@ -512,15 +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: Thu Nov 17 22:58:22 2016 -## Date of summary: Thu Nov 17 22:58:23 2016 +## Date of fit: Fri Nov 18 15:22:08 2016 +## Date of summary: Fri Nov 18 15:22:08 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 0.114 s +## Fitted with method Port using 46 model solutions performed in 0.109 s ## ## Weighting: none ## @@ -572,15 +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: Thu Nov 17 22:58:23 2016 -## Date of summary: Thu Nov 17 22:58:23 2016 +## Date of fit: Fri Nov 18 15:22:08 2016 +## Date of summary: Fri Nov 18 15:22:08 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 0.151 s +## Fitted with method Port using 66 model solutions performed in 0.15 s ## ## Weighting: none ## diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 1446a357..ce149bc5 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -41,7 +41,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> @@ -78,21 +78,21 @@ 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 6251.2433 6291.2435 6315.5160 6331.2438 6347.6524 -## Eigenvalue based 858.2035 903.1770 926.2132 948.1505 960.2181 -## deSolve, compiled 721.0067 739.1361 745.9964 757.2656 758.4913 +## 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 ## max neval cld -## 6364.0611 3 c -## 972.2856 3 b -## 759.7171 3 a</code></pre> +## 6394.1290 3 c +## 947.8008 3 b +## 757.8823 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> <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 8.360665 -## Eigenvalue based 1.252071 +## deSolve, not compiled 8.433585 +## Eigenvalue based 1.202476 ## deSolve, compiled 1.000000</code></pre> </div> <div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> @@ -114,11 +114,11 @@ 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 13.601046 13.602861 13.619563 13.604676 13.628821 -## deSolve, compiled 1.341581 1.346263 1.348298 1.350944 1.351657 -## max neval cld -## 13.65297 3 b -## 1.35237 3 a</code></pre> +## 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 +## max neval cld +## 13.655915 3 b +## 1.383669 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 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 3c3b9c54..53b631b1 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 0ec027f1..6d78194f 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/mkin.html b/docs/articles/mkin.html index 4eed053a..8134287b 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -41,7 +41,7 @@ <h1>mkin - Kinetic evaluation of chemical degradation data</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2016-11-17</h4> + <h4 class="date">2016-11-18</h4> </div> diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index ff62e6df..ae46e2d7 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -8,5 +8,3 @@ colorout setwidth nvimcom rmarkdown -microbenchmark -ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData Binary files differnew file mode 100644 index 00000000..fbc45b28 --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb Binary files differnew file mode 100644 index 00000000..2b71e52b --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx Binary files differnew file mode 100644 index 00000000..bee3222a --- /dev/null +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_1255937aa4f0d68ff78163262b20b976.rdx diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex d34e3805..2e7e2244 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png |
