diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 17:11:50 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-04 17:11:50 +0100 |
| commit | 517d9378284bb4341c1bbce6716b89b341c8b61e (patch) | |
| tree | e4ebb4ac0b7e6c91bd8fdf127b69baf66c4b26d7 | |
| parent | 2bd7610ecb5f4aa2ed564bd0d581adb49a1baa41 (diff) | |
Rebuild docs with updated PR for pkgdown
132 files changed, 405 insertions, 250 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 +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.RData diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb Binary files differindex 42cdbaff..6379ba02 100644 --- a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdb diff --git a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx Binary files differindex 5cced058..71b47f70 100644 --- a/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx +++ b/docs/articles/FOCUS_D_cache/html/fit_449df36a8c1e5c902ad4f45fc76df647.rdx diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData Binary files differindex b170a652..f9619505 100644 --- a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.RData diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb Binary files differindex 5aae8d68..a1934a4a 100644 --- a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdb diff --git a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx Binary files differindex 9ecc2d70..f3ea4998 100644 --- a/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx +++ b/docs/articles/FOCUS_D_cache/html/model_911bdb95adf8c19a8e50c4150b20f2fc.rdx diff --git a/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData Binary files differindex 95ceef43..8637b712 100644 --- a/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData +++ b/docs/articles/FOCUS_D_cache/html/plot_2_3aa531f4c45b3e89e3259e0bb1cf7cf7.RData diff --git a/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData Binary files differindex f04428b9..ac6cd420 100644 --- a/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData +++ b/docs/articles/FOCUS_D_cache/html/plot_7873ad9c0e1495350681617620f6522d.RData diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData Binary files differindex 30ad4f31..3c630373 100644 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData +++ b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-2_dde491510c0c9edffde4573123e5fa3b.RData diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.RData Binary files differdeleted file mode 100644 index 580644b8..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdb Binary files differdeleted file mode 100644 index f8c084a8..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdx Binary files differdeleted file mode 100644 index e0718d0f..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-3_8555aac018c25054a7b7c6e1c3222cbb.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.RData Binary files differdeleted file mode 100644 index 70504d5a..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdb Binary files differdeleted file mode 100644 index 314f58de..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdx Binary files differdeleted file mode 100644 index b11317c6..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-4_c4f4f0bac445d50ee790d1ce8921103e.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.RData Binary files differdeleted file mode 100644 index 8a7ff122..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-5_e12b7460b9b5808704fd83e871da502a.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.RData Binary files differdeleted file mode 100644 index 675d9215..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-6_86fcc5fbb808b9fc011ed172dce76d10.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.RData b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.RData Binary files differdeleted file mode 100644 index 0dcf0e32..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.RData +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdb b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdx b/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_D_cache/html/unnamed-chunk-7_940a932199b6610a3d4e88a8ba9f3d29.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_D_files/figure-html/unnamed-chunk-5-1.png Binary files differdeleted file mode 100644 index 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 using 66 model solutions performed in 0.16 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L_cache/html/__packages b/docs/articles/FOCUS_L_cache/html/__packages deleted file mode 100644 index 8042c1f3..00000000 --- a/docs/articles/FOCUS_L_cache/html/__packages +++ /dev/null @@ -1,8 +0,0 @@ -base -minpack.lm -rootSolve -inline -mkin -knitr -microbenchmark -ggplot2 diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData Binary files differdeleted file mode 100644 index ed0c5a13..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdb Binary files differdeleted file mode 100644 index e3db00f2..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdx Binary files differdeleted file mode 100644 index 70daf843..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-10_17bd4df3f9dbbfdb646235ad948e7903.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.RData Binary files differdeleted file mode 100644 index 6727797f..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdb Binary files differdeleted file mode 100644 index cc81096d..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdx Binary files differdeleted file mode 100644 index 9c4afcfd..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-11_55afc351baf052d70313229bbfe083b1.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.RData Binary files differdeleted file mode 100644 index f1fd1a1e..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdb Binary files differdeleted file mode 100644 index 06f854c7..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdx Binary files differdeleted file mode 100644 index 7fe7b836..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-12_475fd4322218ba45b9d4c6570ce82306.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.RData Binary files differdeleted file mode 100644 index c6df11f0..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-13_fe41237f20ce0e1192c2720eb7747508.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.RData Binary files differdeleted file mode 100644 index cb12b63e..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdb Binary files differdeleted file mode 100644 index 4bc303bf..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdx Binary files differdeleted file mode 100644 index e25dd615..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-14_d1d0018379d20457895c7e55068a1dd4.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.RData Binary files differdeleted file mode 100644 index cca9f00d..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdb Binary files differdeleted file mode 100644 index 504ba4a3..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdx Binary files differdeleted file mode 100644 index 9adbac6d..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-15_455b679cd6cc9762c244b80513c515c8.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.RData Binary files differdeleted file mode 100644 index 0a05f4f5..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-16_f0c16cb42c39ff3e0802b1bed681fcd7.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.RData Binary files differdeleted file mode 100644 index 89b8234c..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdb Binary files differdeleted file mode 100644 index 05a10d06..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdx Binary files differdeleted file mode 100644 index 1c1f9696..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-2_6d7c6df950fe0059e9d9a95eee862d26.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.RData Binary files differdeleted file mode 100644 index 2a76a0d2..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdb Binary files differdeleted file mode 100644 index 9edd1973..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdx Binary files differdeleted file mode 100644 index dbf0a9e4..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-3_b475c6205236b47de3205266a85d05eb.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.RData Binary files differdeleted file mode 100644 index b950c4bc..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-4_4baef7cf5b3c7ae95499feb05dc0e5fa.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.RData Binary files differdeleted file mode 100644 index 59911e29..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdb deleted file mode 100644 index e69de29b..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdx Binary files differdeleted file mode 100644 index 4a053a44..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-5_99a08d47988f0a43ccc269459e2a16f2.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.RData Binary files differdeleted file mode 100644 index 70899dc6..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdb Binary files differdeleted file mode 100644 index f8510279..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdx Binary files differdeleted file mode 100644 index e8b039d3..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-6_f68425c53adf6d973b0313f640ab22c4.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.RData Binary files differdeleted file mode 100644 index 2aac9f45..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdb Binary files differdeleted file mode 100644 index 11549909..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdx Binary files differdeleted file mode 100644 index 1fa42d6e..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-7_7e8f2e6290a4398ce495c06f62b5eb5a.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.RData Binary files differdeleted file mode 100644 index 2d69bb7d..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdb Binary files differdeleted file mode 100644 index 57d39958..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdx Binary files differdeleted file mode 100644 index 4473deeb..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-8_50faede8d3b8c141ad3337c437834082.rdx +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.RData b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.RData Binary files differdeleted file mode 100644 index 231deb0f..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.RData +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdb b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdb Binary files differdeleted file mode 100644 index 609d7b43..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdb +++ /dev/null diff --git a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdx b/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdx Binary files differdeleted file mode 100644 index 6c25eae6..00000000 --- a/docs/articles/FOCUS_L_cache/html/unnamed-chunk-9_4097275e9142f8a1f53afaf3c3c84573.rdx +++ /dev/null diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 09039f62..e1572b17 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.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 --> @@ -72,21 +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 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 b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData Binary files differdeleted file mode 100644 index d11ccf31..00000000 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData +++ /dev/null diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb Binary files differdeleted file mode 100644 index 5ac4f484..00000000 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb +++ /dev/null diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx Binary files differdeleted file mode 100644 index 8983f69e..00000000 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx +++ /dev/null diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData Binary files differindex 8fd3567d..e52d9b7b 100644 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb Binary files differindex 7f4d6c92..ff7ed49e 100644 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx Binary files differindex 7f5f16b7..7ec72c33 100644 --- a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx +++ b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.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 2e7e2244..d34e3805 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 diff --git a/docs/news/index.html b/docs/news/index.html index 7c9b63f7..dc316b7a 100644 --- a/docs/news/index.html +++ b/docs/news/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/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 7d036804..c0690f41 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — DFOP.solution • mkin</title> +<title>Double First-Order in Parallel kinetics — DFOP.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Double First-Order in Parallel kinetics</h1> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index cfe6329b..ad4614fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.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 --> @@ -188,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.316 0.000 0.317 +#> 0.264 0.000 0.262 #> #> $mkinmod #> <mkinmod> model generated with @@ -374,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $cost_notrans #> function (P) @@ -396,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -462,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 15:36:31 2016" +#> [1] "Fri Nov 4 17:08:52 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset @@ -541,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -728,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -750,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -813,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] @@ -889,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1076,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -1098,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1161,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 97af2f9c..13dfa186 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> +<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 1487e2c9..5b36ac74 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> +<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 4571c175..446ce4d7 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_HS_ref_A_to_F • mkin</title> +<title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 7003fa0e..db462f10 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_SFO_ref_A_to_F • mkin</title> +<title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 83edd323..ffc7558e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — FOCUS_2006_datasets • mkin</title> +<title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> </div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 83bca886..fdbf0d1f 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> +<title>First-Order Multi-Compartment kinetics — FOMC.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> First-Order Multi-Compartment kinetics </h1> + <h1>First-Order Multi-Compartment kinetics</h1> </div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 13db29aa..fbe0b590 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> Hockey-Stick kinetics — HS.solution • mkin</title> +<title>Hockey-Stick kinetics — HS.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> Hockey-Stick kinetics </h1> + <h1>Hockey-Stick kinetics</h1> </div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 56c2b48e..553c38b0 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> Indeterminate order rate equation kinetics — IORE.solution • mkin</title> +<title>Indeterminate order rate equation kinetics — IORE.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> Indeterminate order rate equation kinetics </h1> + <h1>Indeterminate order rate equation kinetics</h1> </div> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 8ff5b5ba..2ead8f24 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> Single First-Order kinetics — SFO.solution • mkin</title> +<title>Single First-Order kinetics — SFO.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> Single First-Order kinetics </h1> + <h1>Single First-Order kinetics</h1> </div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 43b6028a..be425d83 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> +<title>Single First-Order Reversible Binding kinetics — SFORB.solution • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> Single First-Order Reversible Binding kinetics </h1> + <h1>Single First-Order Reversible Binding kinetics</h1> </div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 8e491bc9..0a126c5c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — add_err • mkin</title> +<title>Add normally distributed errors to simulated kinetic degradation data — add_err • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Add normally distributed errors to simulated kinetic degradation data</h1> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index a3716060..44a8f4c4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — endpoints • mkin</title> +<title>Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> </div> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 633e0865..97352ff8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> Calculate the geometric mean — geometric_mean • mkin</title> +<title>Calculate the geometric mean — geometric_mean • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -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 --> @@ -72,7 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> Calculate the geometric mean </h1> + <h1>Calculate the geometric mean</h1> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 955b5c58..95fed72e 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — ilr • mkin</title> +<title>Function to perform isometric log-ratio transformation — ilr • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to perform isometric log-ratio transformation</h1> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index b7d59a21..32455baa 100644 --- a/docs/reference/index.html +++ b/docs/reference/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/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d32acb5b..6eb4741b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mccall81_245T • mkin</title> +<title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> </div> @@ -119,8 +122,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:38 2016 -#> Date of summary: Fri Nov 4 15:36:38 2016 +#> Date of fit: Fri Nov 4 17:08:59 2016 +#> Date of summary: Fri Nov 4 17:08:59 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -130,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.886 s +#> Fitted with method Port using 246 model solutions performed in 1.497 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 21a8a8f8..fa131a6d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkin_long_to_wide • mkin</title> +<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Convert a dataframe from long to wide format</h1> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index fe6e47e4..077c0b7d 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkin_wide_to_long • mkin</title> +<title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Convert a dataframe with observations over time into long format</h1> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index f5dd4c88..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.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/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 8d420165..d212e3b2 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinerrmin • mkin</title> +<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Calculate the minimum error to assume in order to pass the variance test</h1> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b298d90a..93185eff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinfit • mkin</title> +<title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Fit a kinetic model to data with one or more state variables</h1> </div> @@ -356,8 +359,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:41 2016 -#> Date of summary: Fri Nov 4 15:36:41 2016 +#> Date of fit: Fri Nov 4 17:09:01 2016 +#> Date of summary: Fri Nov 4 17:09:01 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -433,7 +436,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.244 1.208 0.933 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.256 1.216 0.946 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 7dba1b6d..f328c34a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinmod • mkin</title> +<title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to set up a kinetic model with one or more state variables</h1> </div> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 923abc6d..764f1ab4 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,8 +6,8 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinparplot • mkin</title> +<title>Function to plot the confidence intervals obtained using + list(list("mkinfit")) — mkinparplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +61,12 @@ </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 --> @@ -73,8 +78,8 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to plot the confidence intervals obtained using + list(list("mkinfit"))</h1> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5fe94a8a..921affdc 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinplot • mkin</title> +<title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7eb950a..9f00dab7 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinpredict • mkin</title> +<title>Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Produce predictions from a kinetic model using specific parameters</h1> </div> @@ -272,7 +275,7 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.008 0.024 0.005 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.004 0.028 0.004 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -282,7 +285,7 @@ <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.036 0.000 0.037 </div></pre> +#> 0.052 0.000 0.052 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index a0dcd06d..ae9131ac 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinresplot • mkin</title> +<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to plot residuals stored in an mkin object</h1> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 8424eaab..8bb2ce1c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinsub • mkin</title> +<title>Function to set up a kinetic submodel for one state variable — mkinsub • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to set up a kinetic submodel for one state variable</h1> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5613a720..a21a980b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mmkin • mkin</title> +<title>Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> </div> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index e7158180..52db9bc6 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — plot.mkinfit • mkin</title> +<title>Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot the observed data and the fitted model of an mkinfit object</h1> </div> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef5c04b7..eac31273 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — plot.mmkin • mkin</title> +<title>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c578f4ee..9057114d 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — print.mkinds • mkin</title> +<title>Print mkinds objects — print.mkinds • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Print mkinds objects</h1> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 3f653971..2034ea10 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — print.mkinmod • mkin</title> +<title>Print mkinmod objects — print.mkinmod • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Print mkinmod objects</h1> </div> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c63ba490..e2f845d9 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — schaefer07_complex_case • mkin</title> +<title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Metabolism data set used for checking the software quality of KinGUI</h1> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 241964a7..f67bc1d1 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — summary.mkinfit • mkin</title> +<title>Summary method for class "mkinfit" — summary.mkinfit • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Summary method for class "mkinfit"</h1> </div> @@ -139,8 +142,8 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:49 2016 -#> Date of summary: Fri Nov 4 15:36:49 2016 +#> Date of fit: Fri Nov 4 17:09:10 2016 +#> Date of summary: Fri Nov 4 17:09:10 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 333b3dbf..c6f29582 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — synthetic_data_for_UBA_2014 • mkin</title> +<title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Synthetic datasets for one parent compound with two metabolites</h1> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5ee1e9cc..60208ff4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — transform_odeparms • mkin</title> +<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -61,7 +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 --> @@ -73,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> </div> @@ -146,8 +149,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:50 2016 -#> Date of summary: Fri Nov 4 15:36:50 2016 +#> Date of fit: Fri Nov 4 17:09:11 2016 +#> Date of summary: Fri Nov 4 17:09:11 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -155,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.663 s +#> Fitted with method Port using 153 model solutions performed in 0.638 s #> #> Weighting: none #> diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png Binary files differdeleted file mode 100644 index 09bb687c..00000000 --- a/docs/reference/unknown-10.png +++ /dev/null diff --git a/docs/reference/unknown-2.png b/docs/reference/unknown-2.png Binary files differdeleted file mode 100644 index a26e413f..00000000 --- a/docs/reference/unknown-2.png +++ /dev/null diff --git a/docs/reference/unknown-4.png b/docs/reference/unknown-4.png Binary files differdeleted file mode 100644 index f23ed172..00000000 --- a/docs/reference/unknown-4.png +++ /dev/null diff --git a/docs/reference/unknown-6.png b/docs/reference/unknown-6.png Binary files differdeleted file mode 100644 index dc24d92f..00000000 --- a/docs/reference/unknown-6.png +++ /dev/null diff --git a/docs/reference/unknown-8.png b/docs/reference/unknown-8.png Binary files differdeleted file mode 100644 index e4ab674a..00000000 --- a/docs/reference/unknown-8.png +++ /dev/null |
