diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 16:57:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-09-14 17:00:08 +0200 |
| commit | 70d158c4dd919f4f77bc12f8ace333d29d249b79 (patch) | |
| tree | ab0dd14d85a0c1506262bb6866e2cc49c2400389 /docs | |
| parent | d52e522a9abea09fae1189b066e2a2e1dbb9cb34 (diff) | |
Remove two vignettes from the package but not from docs
- Rebuild static documentation
- Adapt test to new approach to two component error model
where the model is inadequate
Diffstat (limited to 'docs')
63 files changed, 785 insertions, 252 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 3ed8004e..6dde02d4 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -55,10 +55,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -160,10 +160,10 @@ <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">summary</span>(fit)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.1 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Wed Jul 18 14:52:30 2018 -## Date of summary: Wed Jul 18 14:52:31 2018 +## Date of fit: Fri Sep 14 16:50:31 2018 +## Date of summary: Fri Sep 14 16:50:31 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -171,7 +171,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.604 s +## Fitted with method Port using 153 model solutions performed in 0.728 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index cc069d1a..1087c0ed 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -55,10 +55,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -108,17 +108,17 @@ <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> <a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:13 2018 -## Date of summary: Fri Sep 14 11:36:13 2018 +## Date of fit: Fri Sep 14 16:54:49 2018 +## Date of summary: Fri Sep 14 16:54:49 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.085 s +## Fitted with method Port using 37 model solutions performed in 0.088 s ## ## Weighting: none ## @@ -199,17 +199,17 @@ <a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw">plot</span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:14 2018 -## Date of summary: Fri Sep 14 11:36:14 2018 +## Date of fit: Fri Sep 14 16:54:51 2018 +## Date of summary: Fri Sep 14 16:54:51 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.405 s +## Fitted with method Port using 611 model solutions performed in 1.349 s ## ## Weighting: none ## @@ -294,17 +294,17 @@ <a class="sourceLine" id="cb11-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:15 2018 -## Date of summary: Fri Sep 14 11:36:15 2018 +## Date of fit: Fri Sep 14 16:54:51 2018 +## Date of summary: Fri Sep 14 16:54:51 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.188 s +## Fitted with method Port using 81 model solutions performed in 0.18 s ## ## Weighting: none ## @@ -365,10 +365,10 @@ <a class="sourceLine" id="cb14-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:16 2018 -## Date of summary: Fri Sep 14 11:36:16 2018 +## Date of fit: Fri Sep 14 16:54:52 2018 +## Date of summary: Fri Sep 14 16:54:52 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -377,7 +377,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.833 s +## Fitted with method Port using 336 model solutions performed in 0.754 s ## ## Weighting: none ## @@ -457,10 +457,10 @@ <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:17 2018 -## Date of summary: Fri Sep 14 11:36:17 2018 +## Date of fit: Fri Sep 14 16:54:53 2018 +## Date of summary: Fri Sep 14 16:54:53 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -469,7 +469,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.335 s +## Fitted with method Port using 137 model solutions performed in 0.312 s ## ## Weighting: none ## @@ -558,17 +558,17 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><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>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:18 2018 -## Date of summary: Fri Sep 14 11:36:18 2018 +## Date of fit: Fri Sep 14 16:54:54 2018 +## Date of summary: Fri Sep 14 16:54:54 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.099 s +## Fitted with method Port using 46 model solutions performed in 0.098 s ## ## Weighting: none ## @@ -618,17 +618,17 @@ ## DT50 DT90 ## parent 106 352</code></pre> <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><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>)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.47.3 +<pre><code>## mkin version used for fitting: 0.9.47.5 ## R version used for fitting: 3.5.1 -## Date of fit: Fri Sep 14 11:36:18 2018 -## Date of summary: Fri Sep 14 11:36:18 2018 +## Date of fit: Fri Sep 14 16:54:54 2018 +## Date of summary: Fri Sep 14 16:54:54 2018 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.152 s +## Fitted with method Port using 66 model solutions performed in 0.153 s ## ## Weighting: none ## diff --git a/docs/articles/index.html b/docs/articles/index.html index e20ad2d4..ad0ab46e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -84,10 +84,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -123,10 +123,10 @@ <ul> <li><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> <li><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> - <li><a href="FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li> - <li><a href="compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> <li><a href="mkin.html">Introduction to mkin</a></li> <li><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li> + <li><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> </ul> </div> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index bc76c2cf..3ae09165 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -55,10 +55,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index a2f7f72a..4d516ff1 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -29,7 +29,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -55,10 +55,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html new file mode 100644 index 00000000..381c9e4f --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z.html @@ -0,0 +1,332 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<title>Example evaluation of FOCUS dataset Z 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<li> + <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="../../news/index.html">News</a> +</li> + </ul> +<ul class="nav navbar-nav navbar-right"></ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <h1>Example evaluation of FOCUS dataset Z</h1> + <h4 class="author">Johannes Ranke</h4> + + <h4 class="date">2018-09-14</h4> + + + <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> + + </div> + + + +<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> +<div id="the-data" class="section level1"> +<h1 class="hasAnchor"> +<a href="#the-data" class="anchor"></a>The data</h1> +<p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" data-line-number="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a> +<a class="sourceLine" id="cb1-3" data-line-number="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw">data.frame</span>(</a> +<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> +<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a> +<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">Z0 =</span> <span class="kw">c</span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> +<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a> +<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">Z1 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> +<a class="sourceLine" id="cb1-9" data-line-number="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> +<a class="sourceLine" id="cb1-10" data-line-number="10"> <span class="dt">Z2 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> +<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> +<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">Z3 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> +<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a> +<a class="sourceLine" id="cb1-14" data-line-number="14"></a> +<a class="sourceLine" id="cb1-15" data-line-number="15">FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div> +</div> +<div id="parent-and-one-metabolite" class="section level1"> +<h1 class="hasAnchor"> +<a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1> +<p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> +<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA +## k_Z0_sink 1.2790e-11 0.226895 5.6368e-11 5.0000e-01 NA NA +## k_Z0_Z1 2.2360e+00 0.165073 1.3546e+01 7.3938e-14 NA NA +## k_Z1_sink 4.8212e-01 0.065854 7.3212e+00 3.5520e-08 NA NA</code></pre> +<p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> +<p>A similar result can be obtained when formation fractions are used in the model formulation:</p> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA +## k_Z0 2.23601 0.216849 10.3114 3.6623e-11 NA NA +## k_Z1 0.48212 0.065854 7.3211 3.5520e-08 NA NA +## f_Z0_to_Z1 1.00000 0.101473 9.8548 9.7068e-11 NA NA</code></pre> +<p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> +<p>A simplified model is obtained by removing the pathway to the sink. </p> +<p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb12-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508 +## k_Z0 2.23601 0.146861 15.225 2.2464e-15 1.95453 2.558 +## k_Z1 0.48212 0.042687 11.294 3.0686e-12 0.40216 0.578</code></pre> +<p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> +</div> +<div id="metabolites-z2-and-z3" class="section level1"> +<h1 class="hasAnchor"> +<a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> +<p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb17-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb17-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> +<p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> +<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb20-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb20-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb20-5" data-line-number="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb22-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb22-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge: +## false convergence (8)</code></pre> +<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw">summary</span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445 +## k_Z0 2.215368 0.118098 18.7587 7.6563e-25 1.990525 2.465609 +## k_Z1 0.478302 0.029289 16.3302 3.3408e-22 0.422977 0.540864 +## k_Z2 0.451617 0.044214 10.2144 3.1133e-14 0.371034 0.549702 +## k_Z3 0.058693 0.014296 4.1056 7.2924e-05 0.035994 0.095705 +## f_Z2_to_Z3 0.471516 0.057057 8.2639 2.8156e-11 0.360381 0.585548</code></pre> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> +<pre><code>## $ff +## Z2_Z3 Z2_sink +## 0.47152 0.52848 +## +## $SFORB +## logical(0) +## +## $distimes +## DT50 DT90 +## Z0 0.31288 1.0394 +## Z1 1.44918 4.8141 +## Z2 1.53481 5.0985 +## Z3 11.80973 39.2311</code></pre> +<p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> +</div> +<div id="using-the-sforb-model" class="section level1"> +<h1 class="hasAnchor"> +<a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> +<p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> +<p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb29-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb29-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb29-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb31-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw">summary</span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> +<pre><code>## NULL</code></pre> +<p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb34-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb34-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" data-line-number="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb36-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> +<p>This results in a much better representation of the behaviour of the parent compound Z0.</p> +<p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> +<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb37-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb39-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb39-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb39-4" data-line-number="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> +<p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> +<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb40-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb40-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb40-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb42-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> +<a class="sourceLine" id="cb42-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb42-4" data-line-number="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> +<p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb43-2" data-line-number="2"> <span class="dt">parms.ini =</span> <span class="kw">c</span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> +<a class="sourceLine" id="cb43-3" data-line-number="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb43-4" data-line-number="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> +<a class="sourceLine" id="cb43-5" data-line-number="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb43-6" data-line-number="6"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> +<p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> +<p>A graphical representation of the confidence intervals can finally be obtained.</p> +<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> +<p>The endpoints obtained with this model are</p> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<pre><code>## $ff +## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink +## 1.00000 1.00000 0.46344 0.53656 1.00000 +## +## $SFORB +## Z0_b1 Z0_b2 Z3_b1 Z3_b2 +## 2.4471382 0.0075127 0.0800075 0.0000000 +## +## $distimes +## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 +## Z0 0.3043 1.1848 0.28325 92.264 NA NA +## Z1 1.5148 5.0320 NA NA NA NA +## Z2 1.6414 5.4526 NA NA NA NA +## Z3 NA NA NA NA 8.6635 Inf</code></pre> +<p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> +</div> +<div id="references" class="section level1"> +<h1 class="hasAnchor"> +<a href="#references" class="anchor"></a>References</h1> +<!-- vim: set foldmethod=syntax: --> +<div id="refs" class="references"> +<div id="ref-FOCUSkinetics2014"> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +</div> +</div> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> + <h2 class="hasAnchor"> +<a href="#tocnav" class="anchor"></a>Contents</h2> + <ul class="nav nav-pills nav-stacked"> +<li><a href="#the-data">The data</a></li> + <li><a href="#parent-and-one-metabolite">Parent and one metabolite</a></li> + <li><a href="#metabolites-z2-and-z3">Metabolites Z2 and Z3</a></li> + <li><a href="#using-the-sforb-model">Using the SFORB model</a></li> + <li><a href="#references">References</a></li> + </ul> +</div> + </div> + +</div> + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> +</div> + + + + </body> +</html> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differnew file mode 100644 index 00000000..53f2ce85 --- /dev/null +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differnew file 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</li> + <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="../../news/index.html">News</a> +</li> + </ul> +<ul class="nav navbar-nav navbar-right"></ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> + + + </header><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <h1>Performance benefit by using compiled model definitions in mkin</h1> + <h4 class="author">Johannes Ranke</h4> + + <h4 class="date">2018-09-14</h4> + + + <div class="hidden name"><code>compiled_models.Rmd</code></div> + + </div> + + + +<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2"> +<h2 class="hasAnchor"> +<a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2> +<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</a></code></pre></div> +<pre><code>## gcc +## "/usr/bin/gcc"</code></pre> +<p>First, we build a simple degradation model for a parent compound with one metabolite.</p> +<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a> +<a class="sourceLine" id="cb5-2" data-line-number="2"> b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> +<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a> +<a class="sourceLine" id="cb5-5" data-line-number="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-6" data-line-number="6"> <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-7" data-line-number="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-8" data-line-number="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-9" data-line-number="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> +<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.1</span>)</a> +<a class="sourceLine" id="cb5-12" data-line-number="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> +<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb5-14" data-line-number="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> +<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> +<pre><code>## Lade nötiges Paket: rbenchmark</code></pre> +<pre><code>## test replications elapsed relative user.self sys.self +## 3 deSolve, compiled 3 2.120 1.000 2.118 0.000 +## 1 deSolve, not compiled 3 17.195 8.111 17.187 0.000 +## 2 Eigenvalue based 3 2.589 1.221 2.582 0.004 +## user.child sys.child +## 3 0 0 +## 1 0 0 +## 2 0 0</code></pre> +<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> +</div> +<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> +<h2 class="hasAnchor"> +<a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> +<p>This evaluation is also taken from the example section of mkinfit.</p> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a> +<a class="sourceLine" id="cb8-2" data-line-number="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb8-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> +<a class="sourceLine" id="cb8-5" data-line-number="5"></a> +<a class="sourceLine" id="cb8-6" data-line-number="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> +<a class="sourceLine" id="cb8-7" data-line-number="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb8-9" data-line-number="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb8-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> +<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.2</span>)</a> +<a class="sourceLine" id="cb8-12" data-line-number="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> +<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb8-14" data-line-number="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> +<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<pre><code>## test replications elapsed relative user.self sys.self +## 2 deSolve, compiled 3 3.761 1.000 3.758 0.000 +## 1 deSolve, not compiled 3 36.462 9.695 36.441 0.004 +## user.child sys.child +## 2 0 0 +## 1 0 0</code></pre> +<p>Here we get a performance benefit of a factor of 10 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 0.9.47.5 on</p> +<pre><code>## R version 3.5.1 (2018-07-02) +## Platform: x86_64-pc-linux-gnu (64-bit) +## Running under: Debian GNU/Linux 9 (stretch)</code></pre> +<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> + <h2 class="hasAnchor"> +<a href="#tocnav" class="anchor"></a>Contents</h2> + <ul class="nav nav-pills nav-stacked"> +<li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li> + <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li> + </ul> +</div> + </div> + +</div> + + + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> +</div> + + + + </body> +</html> diff --git a/docs/authors.html b/docs/authors.html index 61cf4fbc..fddc66c9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -84,10 +84,10 @@ <a href="articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/index.html b/docs/index.html index 5a3864bf..60787c81 100644 --- a/docs/index.html +++ b/docs/index.html @@ -36,7 +36,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -62,10 +62,10 @@ <a href="articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/news/index.html b/docs/news/index.html index 6cc7351d..4bd93964 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -84,10 +84,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 8da0943f..bbd8704e 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -4,8 +4,8 @@ pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html FOCUS_L: FOCUS_L.html - FOCUS_Z: FOCUS_Z.html - compiled_models: compiled_models.html mkin: mkin.html twa: twa.html + FOCUS_Z: web_only/FOCUS_Z.html + compiled_models: web_only/compiled_models.html diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 2f714f2c..f3ee0099 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 922479a1..9d49313c 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.164 0.000 0.164 +#> 0.169 0.000 0.169 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd535f0> -#> <environment: 0x55555bd1c770> +#> <bytecode: 0x55555bd4a710> +#> <environment: 0x55555bd3c748> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c9c70f8> -#> <environment: 0x55555bd1c770> +#> <bytecode: 0x55555c9b4488> +#> <environment: 0x55555bd3c748> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,10 +558,10 @@ #> 99.17407 #> #> $date -#> [1] "Fri Sep 14 11:34:38 2018" +#> [1] "Fri Sep 14 16:53:13 2018" #> #> $version -#> [1] "0.9.47.4" +#> [1] "0.9.47.5" #> #> $Rversion #> [1] "3.5.1" 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 bea35e09..d5354c28 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> 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 9122a546..f5c36792 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> 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 3d5677e8..fb2cd7de 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> 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 524fbd79..dfccea5c 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -65,7 +65,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index a0bcc65d..7f89e33e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 10f33260..abda4d81 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ The form given here differs slightly from the original reference by Gustafson <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index cb9eb353..bb3768ba 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 23f82d13..d86ee0c3 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 087ff46f..17f1920c 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 61989c40..050d19cf 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index b3324064..cea1e03c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -89,10 +89,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index fdf465a5..a54fb71e 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -90,10 +90,10 @@ with the advantage that the SFORB model can also be used for metabolites." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index bddbab1a..41ccbbfd 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index e780d26b..601ab1a2 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/index.html b/docs/reference/index.html index 185991d6..615f6777 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -58,7 +58,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -84,10 +84,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index ef7209bf..3a19c754 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -65,7 +65,7 @@ guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ guidance." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index ac2adf1e..86f3c07e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -89,10 +89,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -156,10 +156,10 @@ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 + <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:34:50 2018 -#> Date of summary: Fri Sep 14 11:34:50 2018 +#> Date of fit: Fri Sep 14 16:53:25 2018 +#> Date of summary: Fri Sep 14 16:53:25 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.33 s +#> Fitted with method Port using 574 model solutions performed in 3.403 s #> #> Weighting: none #> @@ -245,10 +245,10 @@ <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <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 used for fitting: 0.9.47.4 + <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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:34:51 2018 -#> Date of summary: Fri Sep 14 11:34:51 2018 +#> Date of fit: Fri Sep 14 16:53:27 2018 +#> Date of summary: Fri Sep 14 16:53:27 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.417 s +#> Fitted with method Port using 246 model solutions performed in 1.46 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index b83287ff..ea74ff47 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -89,10 +89,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index e2b4ef61..369649e3 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index c77945b9..d356fdab 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index a18b226e..4f70a274 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 13029e91..0f2bb875 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -97,10 +97,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -432,17 +432,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> <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 used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:34:54 2018 -#> Date of summary: Fri Sep 14 11:34:54 2018 +#> Date of fit: Fri Sep 14 16:53:29 2018 +#> Date of summary: Fri Sep 14 16:53:29 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.141 s +#> Fitted with method Port using 64 model solutions performed in 0.158 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ <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 verstrichen -#> 0.906 0.000 0.907 </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 +#> 0.909 0.000 0.910 </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 @@ -586,7 +586,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.714 0.000 0.715 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.749 0.000 0.749 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</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.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -622,10 +622,10 @@ </div><div class='input'><span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:05 2018 -#> Date of summary: Fri Sep 14 11:35:05 2018 +#> Date of fit: Fri Sep 14 16:53:40 2018 +#> Date of summary: Fri Sep 14 16:53:40 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +633,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.763 s +#> Fitted with method Port using 186 model solutions performed in 0.79 s #> #> Weighting: none #> @@ -739,10 +739,10 @@ #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:07 2018 -#> Date of summary: Fri Sep 14 11:35:07 2018 +#> Date of fit: Fri Sep 14 16:53:43 2018 +#> Date of summary: Fri Sep 14 16:53:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +750,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.297 s +#> Fitted with method Port using 551 model solutions performed in 2.278 s #> #> Weighting: none #> @@ -861,10 +861,10 @@ #> 100 m1 33.13 31.98971 1.140e+00 2.722 #> 120 m1 25.15 28.80898 -3.659e+00 2.722 #> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:08 2018 -#> Date of summary: Fri Sep 14 11:35:08 2018 +#> Date of fit: Fri Sep 14 16:53:43 2018 +#> Date of summary: Fri Sep 14 16:53:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +872,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.618 s +#> Fitted with method Port using 155 model solutions performed in 0.643 s #> #> Weighting: mean #> @@ -979,10 +979,10 @@ #> 120 m1 25.15 28.82413 -3.674128 #> 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:09 2018 -#> Date of summary: Fri Sep 14 11:35:09 2018 +#> Date of fit: Fri Sep 14 16:53:44 2018 +#> Date of summary: Fri Sep 14 16:53:44 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +990,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.704 s +#> Fitted with method Port using 174 model solutions performed in 0.722 s #> #> Weighting: manual #> @@ -1099,10 +1099,10 @@ <span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:10 2018 -#> Date of summary: Fri Sep 14 11:35:10 2018 +#> Date of fit: Fri Sep 14 16:53:45 2018 +#> Date of summary: Fri Sep 14 16:53:45 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1110,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.109 s +#> Fitted with method Port using 270 model solutions performed in 1.11 s #> #> Weighting: manual #> @@ -1217,10 +1217,10 @@ #> 120 m1 25.15 28.76062 -3.610621 2 #> 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:13 2018 -#> Date of summary: Fri Sep 14 11:35:13 2018 +#> Date of fit: Fri Sep 14 16:53:49 2018 +#> Date of summary: Fri Sep 14 16:53:49 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1228,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 2.903 s +#> Fitted with method Port using 692 model solutions performed in 2.945 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 857e0c74..3633686e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -92,10 +92,10 @@ For the definition of model types and their parameters, the equations given <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file3c104e6e45e4.c 2> file3c104e6e45e4.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file7b505448f8a5.c 2> file7b505448f8a5.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index adcd2a3b..6ed32315 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 2d878175..72ff93f6 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index ffd6e89f..6c30d7a8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -89,10 +89,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -326,7 +326,7 @@ <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='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.002 </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='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 diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index b4e1e747..306b7400 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -90,10 +90,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index a34f1dae..0a2bf41a 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 621571c1..a656ef65 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -189,8 +189,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.046 0.033 6.654 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 20.150 0.000 20.163 </div><div class='input'> +#> 0.054 0.029 6.762 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 20.495 0.004 20.512 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4fec74c9..e88c2025 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -66,7 +66,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -92,10 +92,10 @@ If the current plot device is a tikz device, <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 478a5682..d67d87d9 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -65,7 +65,7 @@ If the current plot device is a tikz device, </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -91,10 +91,10 @@ If the current plot device is a tikz device, <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index f59325f9..2489269c 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 299fdfbb..b6cbad61 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -61,7 +61,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -87,10 +87,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 9fd60805..4ceba867 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -89,10 +89,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 6db7d74c..e74707ff 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -92,10 +92,10 @@ This is the error model used for example by Werner et al. (1978). The model <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 1d0a7c52..bb701470 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -90,10 +90,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -204,17 +204,17 @@ <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'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.4 + <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'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:35:59 2018 -#> Date of summary: Fri Sep 14 11:35:59 2018 +#> Date of fit: Fri Sep 14 16:54:36 2018 +#> Date of summary: Fri Sep 14 16:54:36 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.076 s +#> Fitted with method Port using 35 model solutions performed in 0.077 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 25cfc012..384d628d 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -102,10 +102,10 @@ Compare also the code in the example section to see the degradation models." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index a30161a2..094e003d 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -62,7 +62,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -88,10 +88,10 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c0ca534c..38c3fe9d 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span> </span> </div> @@ -95,10 +95,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> - <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> @@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='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 used for fitting: 0.9.47.4 +<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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:36:07 2018 -#> Date of summary: Fri Sep 14 11:36:07 2018 +#> Date of fit: Fri Sep 14 16:54:43 2018 +#> Date of summary: Fri Sep 14 16:54:43 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.627 s +#> Fitted with method Port using 153 model solutions performed in 0.629 s #> #> Weighting: none #> @@ -274,10 +274,10 @@ The transformation of sets of formation fractions is fragile, as it supposes #> parent 7.023 23.33 #> m1 131.761 437.70</div><div class='input'> </div><div class='input'><span class='no'>fit.2</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'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 used for fitting: 0.9.47.4 +<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 used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:36:08 2018 -#> Date of summary: Fri Sep 14 11:36:08 2018 +#> Date of fit: Fri Sep 14 16:54:45 2018 +#> Date of summary: Fri Sep 14 16:54:45 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.437 s +#> Fitted with method Port using 350 model solutions performed in 1.426 s #> #> Weighting: none #> @@ -362,10 +362,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>m1</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='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:36:09 2018 -#> Date of summary: Fri Sep 14 11:36:09 2018 +#> Date of fit: Fri Sep 14 16:54:46 2018 +#> Date of summary: Fri Sep 14 16:54:46 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.773 s +#> Fitted with method Port using 186 model solutions performed in 0.766 s #> #> Weighting: none #> @@ -446,10 +446,10 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</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.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 11:36:10 2018 -#> Date of summary: Fri Sep 14 11:36:10 2018 +#> Date of fit: Fri Sep 14 16:54:46 2018 +#> Date of summary: Fri Sep 14 16:54:46 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.424 s +#> Fitted with method Port using 104 model solutions performed in 0.42 s #> #> Weighting: none #> |
