diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-06-05 17:03:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-06-05 17:03:19 +0200 |
| commit | 5243ac0ebe3223e5803b4ebee1cb619008638785 (patch) | |
| tree | 6be4e8e47f8735f4bbce23d8abf328a700e028d8 /docs | |
| parent | b061a00ba4f9410a4b77e58a96fb7baa1247252b (diff) | |
| parent | 4b323789265213bd65165873e7efe5e45a579275 (diff) | |
Merge branch 'algorithm'
Diffstat (limited to 'docs')
141 files changed, 780 insertions, 421 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index ba694065..be1f40f5 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -166,10 +166,10 @@ <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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:27 2019 -## Date of summary: Wed May 8 20:52:27 2019 +## Date of fit: Wed Jun 5 15:10:49 2019 +## Date of summary: Wed Jun 5 15:10:50 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -177,10 +177,11 @@ ## ## Model predictions using solution type deSolve ## -## Fitted using 389 model solutions performed in 0.998 s +## Fitted using 389 model solutions performed in 0.984 s ## -## Error model: -## Constant variance +## Error model: Constant variance +## +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -305,7 +306,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex 0cd6596d..fc1142ab 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex 64da1d2e..97c61a16 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 6771bf63..4388edd2 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -112,20 +112,21 @@ <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" title="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" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:29 2019 -## Date of summary: Wed May 8 20:52:29 2019 +## Date of fit: Wed Jun 5 15:10:52 2019 +## Date of summary: Wed Jun 5 15:10:52 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.276 s +## Fitted using 133 model solutions performed in 0.277 s ## -## Error model: -## Constant variance +## Error model: Constant variance +## +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -213,10 +214,10 @@ <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> -<pre><code>## mkin version used for fitting: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:31 2019 -## Date of summary: Wed May 8 20:52:31 2019 +## Date of fit: Wed Jun 5 15:10:54 2019 +## Date of summary: Wed Jun 5 15:10:54 2019 ## ## ## Warning: Optimisation did not converge: @@ -228,10 +229,11 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.868 s +## Fitted using 899 model solutions performed in 1.877 s +## +## Error model: Constant variance ## -## Error model: -## Constant variance +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -317,20 +319,21 @@ <a class="sourceLine" id="cb16-3" title="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="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:32 2019 -## Date of summary: Wed May 8 20:52:32 2019 +## Date of fit: Wed Jun 5 15:10:55 2019 +## Date of summary: Wed Jun 5 15:10:55 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.483 s +## Fitted using 239 model solutions performed in 0.492 s ## -## Error model: -## Constant variance +## Error model: Constant variance +## +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -392,10 +395,10 @@ <a class="sourceLine" id="cb19-3" title="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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:33 2019 -## Date of summary: Wed May 8 20:52:33 2019 +## Date of fit: Wed Jun 5 15:10:56 2019 +## Date of summary: Wed Jun 5 15:10:56 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -404,10 +407,11 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 1.185 s +## Fitted using 572 model solutions performed in 1.183 s +## +## Error model: Constant variance ## -## Error model: -## Constant variance +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -491,10 +495,10 @@ <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="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> -<pre><code>## mkin version used for fitting: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:35 2019 -## Date of summary: Wed May 8 20:52:35 2019 +## Date of fit: Wed Jun 5 15:10:58 2019 +## Date of summary: Wed Jun 5 15:10:58 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -503,10 +507,11 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.768 s +## Fitted using 373 model solutions performed in 0.773 s ## -## Error model: -## Constant variance +## Error model: Constant variance +## +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -596,20 +601,21 @@ <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="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:36 2019 -## Date of summary: Wed May 8 20:52:37 2019 +## Date of fit: Wed Jun 5 15:10:59 2019 +## Date of summary: Wed Jun 5 15:10:59 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.289 s +## Fitted using 142 model solutions performed in 0.288 s +## +## Error model: Constant variance ## -## Error model: -## Constant variance +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -660,20 +666,21 @@ ## DT50 DT90 ## parent 106 352</code></pre> <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.4 +<pre><code>## mkin version used for fitting: 0.9.49.5 ## R version used for fitting: 3.6.0 -## Date of fit: Wed May 8 20:52:36 2019 -## Date of summary: Wed May 8 20:52:37 2019 +## Date of fit: Wed Jun 5 15:10:59 2019 +## Date of summary: Wed Jun 5 15:10:59 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.45 s +## Fitted using 224 model solutions performed in 0.453 s +## +## Error model: Constant variance ## -## Error model: -## Constant variance +## Error model algorithm: d_3 ## ## Starting values for parameters to be optimised: ## value type @@ -769,7 +776,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png Binary files differindex cc28c092..32fef506 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png Binary files differindex 46d85b73..f23a4c97 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png Binary files differindex ac326b45..ed6a781d 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-13-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differindex 62b2ceb3..2e5071d9 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png Binary files differindex 1a9c8457..04bee502 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-4-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png Binary files differindex 93beb55f..86af1cf9 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-5-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex 3dd8565c..16235059 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png Binary files differindex 8d6531ea..0bfac9e2 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png Binary files differindex a5e75b70..d194c676 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index eb2d55ef..c2982f4b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -60,7 +60,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -145,7 +145,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index c274696c..5977d642 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>mkin.Rmd</code></div> @@ -243,7 +243,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex 29ae1c43..751a79e1 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 9f660fab..f98026e7 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>twa.Rmd</code></div> @@ -139,7 +139,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 9184fad5..542deb14 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -377,7 +377,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> 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 differindex 0880ca60..471db177 100644 --- 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 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 differindex 1a92365e..3c983f21 100644 --- 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 diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex debf3cb8..0e0a78a9 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex 89020a0a..d7dd85a5 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex 8188c4cf..7764f4e2 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png Binary files differindex 8e13b498..d24b8a40 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png Binary files differindex 7d490baa..dd8c1e0a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex 4916ee4d..45a32027 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex a11e0092..18832ed2 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differindex 292c0690..0d3b4d1a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex acd197f2..898e6190 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 4d9e9b2d..4cd16437 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -308,16 +308,11 @@ <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> <div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb30"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb30-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -327,11 +322,10 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.16549 NA NA NA -## k__iore_parent_sink 0.00100 NA NA NA -## k_parent_sink 0.00803 NA NA NA -## sigma 7.44786 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 88.16549 6.53e-29 83.37344 92.95754 +## k_parent_sink 0.00803 1.67e-13 0.00674 0.00957 +## sigma 7.44786 4.17e-10 5.66209 9.23363 ## ## $IORE ## Estimate Pr(>t) Lower Upper @@ -341,13 +335,12 @@ ## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 95.70619 NA NA NA -## k__iore_parent_sink 0.00100 NA NA NA -## k1 0.02500 NA NA NA -## k2 0.00273 NA NA NA -## g 0.58835 NA NA NA -## sigma 3.90001 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.70619 8.99e-32 91.87941 99.53298 +## k1 0.02500 5.25e-04 0.01422 0.04394 +## k2 0.00273 6.84e-03 0.00125 0.00597 +## g 0.58835 2.84e-06 0.36595 0.77970 +## sigma 3.90001 6.94e-10 2.96260 4.83741 ## ## ## DTx values: @@ -366,12 +359,12 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -415,7 +408,7 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> @@ -423,9 +416,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -469,12 +462,12 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -522,12 +515,12 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -576,14 +569,14 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no ## covariance matrix</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -626,7 +619,7 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> @@ -637,9 +630,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -682,16 +675,16 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -735,16 +728,16 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -788,7 +781,7 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb98"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb98-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> @@ -796,9 +789,9 @@ ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -837,16 +830,16 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- ## finite result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -890,14 +883,14 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -1010,7 +1003,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex f84439e8..291b48e1 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p11-1.png Binary files differindex 2f659bca..149cf24c 100644 --- 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a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index a53f1927..507bdb61 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -115,32 +115,32 @@ <a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a> <a class="sourceLine" id="cb2-2" title="2">t1 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb2-4" title="4"></a> -<a class="sourceLine" id="cb2-5" title="5"><span class="co"># One metabolite</span></a> -<a class="sourceLine" id="cb2-6" title="6">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb2-7" title="7"> <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="cb2-8" title="8"> <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> +<a class="sourceLine" id="cb2-3" title="3">t2 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: +## iteration limit reached without convergence (10)</code></pre> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># One metabolite</span></a> +<a class="sourceLine" id="cb4-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb4-3" title="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="cb4-4" title="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> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb4-2" title="2"> <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="cb4-3" title="3"> <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> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> <a class="sourceLine" id="cb6-2" title="2"> <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="cb6-3" title="3"> <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> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">DFOP_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb8-2" title="2"> <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="cb8-3" title="3"> <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> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t3 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): +## Observations with value of zero were removed from the data</code></pre> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): -## Observations with value of zero were removed from the data - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> -<a class="sourceLine" id="cb10-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">t4 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a> +<a class="sourceLine" id="cb13-2" title="2">t5 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div> <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data @@ -149,117 +149,131 @@ ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): ## Observations with value of zero were removed from the data</code></pre> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> -<a class="sourceLine" id="cb12-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb12-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb12-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-6" title="6"></a> -<a class="sourceLine" id="cb12-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> -<a class="sourceLine" id="cb12-8" title="8"> <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="cb12-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb12-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb12-11" title="11"></a> -<a class="sourceLine" id="cb12-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-13" title="13"></a> -<a class="sourceLine" id="cb12-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> -<a class="sourceLine" id="cb12-15" title="15"></a> -<a class="sourceLine" id="cb12-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-18" title="18"></a> -<a class="sourceLine" id="cb12-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-21" title="21"></a> -<a class="sourceLine" id="cb12-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> -<a class="sourceLine" id="cb12-24" title="24"></a> -<a class="sourceLine" id="cb12-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> -<a class="sourceLine" id="cb12-26" title="26">mkin_benchmarks</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a> +<a class="sourceLine" id="cb15-2" title="2">m_synth_SFO_lin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> +<a class="sourceLine" id="cb15-3" title="3"> <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> +<a class="sourceLine" id="cb15-4" title="4"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-6" title="6"></a> +<a class="sourceLine" id="cb15-7" title="7">m_synth_DFOP_par <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a> +<a class="sourceLine" id="cb15-8" title="8"> <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="cb15-9" title="9"> <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb15-10" title="10"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb15-11" title="11"></a> +<a class="sourceLine" id="cb15-12" title="12">SFO_lin_a <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-13" title="13"></a> +<a class="sourceLine" id="cb15-14" title="14">DFOP_par_c <-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a> +<a class="sourceLine" id="cb15-15" title="15"></a> +<a class="sourceLine" id="cb15-16" title="16">t6 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-17" title="17">t7 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-18" title="18"></a> +<a class="sourceLine" id="cb15-19" title="19">t8 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-20" title="20">t9 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-21" title="21"></a> +<a class="sourceLine" id="cb15-22" title="22">t10 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-23" title="23">t11 <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a> +<a class="sourceLine" id="cb15-24" title="24"></a> +<a class="sourceLine" id="cb15-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a> +<a class="sourceLine" id="cb15-26" title="26">mkin_benchmarks</a></code></pre></div> <pre><code>## CPU ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 AMD Ryzen 7 1700 Eight-Core Processor ## OS ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 Linux ## mkin ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 0.9.49.5 ## t1 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.792 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.828 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 17.398 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.869 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.412 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 16.104 -## t5 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.527 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.497 +## t5 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.329 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.541 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.548 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.308 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.192 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.775 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.827 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.116 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.653 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.063 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.762 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.784</code></pre> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.512</code></pre> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> @@ -281,7 +295,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index f296c8a4..5f0301fc 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -30,7 +30,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -88,7 +88,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-05-08</h4> + <h4 class="date">2019-06-05</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -163,9 +163,9 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.131 1.000 3.129 0 -## 1 deSolve, not compiled 3 28.306 9.041 28.290 0 -## 2 Eigenvalue based 3 4.361 1.393 4.358 0 +## 3 deSolve, compiled 3 3.041 1.000 3.039 0 +## 1 deSolve, not compiled 3 28.429 9.349 28.415 0 +## 2 Eigenvalue based 3 4.291 1.411 4.288 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -214,16 +214,16 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 5.023 1.000 5.021 0 -## 1 deSolve, not compiled 3 53.267 10.605 53.235 0 +## 2 deSolve, compiled 3 4.927 1.000 4.924 0 +## 1 deSolve, not compiled 3 53.138 10.785 53.108 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.49.4 on</p> +<p>This vignette was built with mkin 0.9.49.5 on</p> <pre><code>## R version 3.6.0 (2019-04-26) ## Platform: x86_64-pc-linux-gnu (64-bit) -## Running under: Debian GNU/Linux 9 (stretch)</code></pre> +## Running under: Debian GNU/Linux 10 (buster)</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> </div> @@ -247,7 +247,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/authors.html b/docs/authors.html index 9d47c66a..61f965ce 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -60,7 +60,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -151,7 +151,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/index.html b/docs/index.html index 2f494511..e3f3b376 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -205,7 +205,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/news/index.html b/docs/news/index.html index 11414ed3..df6d53db 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -122,13 +122,14 @@ </div> - <div id="mkin-0-9-49-4-2019-05-08" class="section level1"> + <div id="mkin-0-9-49-5-2019-06-04" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-49-4-2019-05-08" class="anchor"></a>mkin 0.9.49.4 (2019-05-08)<small> Unreleased </small> +<a href="#mkin-0-9-49-5-2019-06-04" class="anchor"></a>mkin 0.9.49.5 (2019-06-04)<small> Unreleased </small> </h1> <ul> -<li><p>Direct minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable</p></li> -<li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ instead</p></li> +<li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm tries direct minimization and a three step procedure, and returns the model with the highest likelihood.</p></li> +<li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead</p></li> +<li><p>Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.</p></li> <li><p>New function ‘mkinerrplot’. This function is also used for residual plots in ‘plot.mmkin’ if the argument ‘resplot = “errmod”’ is given, and in ‘plot.mkinfit’ if ‘show_errplot’ is set to TRUE.</p></li> <li><p>Remove dependency on FME, only use nlminb for optimisation</p></li> <li><p>Use the numDeriv package to calculate hessians</p></li> @@ -136,6 +137,7 @@ <li><p>The code for manual weighting was removed</p></li> <li><p>The fitting time reported in the summary now includes the calculation of the hessians</p></li> <li><p>Adapt tests</p></li> +<li><p>Fix an error in the FOCUS chi2 error level calculations that occurred if parameters were specified in parms.ini that were not in the model. A warning was already issued, but when fitting via mmkin this could easily go unnoticed.</p></li> </ul> </div> <div id="mkin-0-9-48-1-2019-03-04" class="section level1"> @@ -696,7 +698,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-49-4-2019-05-08">0.9.49.4</a></li> + <li><a href="#mkin-0-9-49-5-2019-06-04">0.9.49.5</a></li> <li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> @@ -740,7 +742,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index eda9c58f..db7859c8 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.2.1 -pkgdown: 1.3.0.9000 +pkgdown: 1.3.0 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index c797567c..a5626847 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -201,7 +201,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index e4ed9cda..5db220ee 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -232,7 +232,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 0fbc1da1..a2d75ccc 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 335c3a80..edfa70d3 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -199,7 +199,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 652dfee0..37c0b361 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -172,16 +172,16 @@ <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'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset #> model B C -#> FOMC List,36 List,36 +#> FOMC List,37 List,37 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,36 -#> FOMC List,36 +#> SFO List,37 +#> FOMC List,37 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,36 +#> SFO List,37 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>( @@ -229,7 +229,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> 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 047a5f4d..b1165f1d 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -67,7 +67,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -187,7 +187,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index cc3560ed..03a15a5a 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -186,7 +186,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 5f6fc197..6046ec88 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -187,7 +187,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 45d00237..278425f6 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -185,7 +185,7 @@ in this fit.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 2b060f47..0d29deb2 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -183,7 +183,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex 127f3085..aa41a253 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 90a4810c..69c0a9ef 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -67,7 +67,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -213,7 +213,7 @@ The form given here differs slightly from the original reference by Gustafson </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex 4dc42c31..ae056d9b 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 1365e23f..e14f80ec 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -200,7 +200,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex d8b6e8e3..00e28460 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index c67c2a37..ca0db0bb 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -214,7 +214,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex bcf5d12c..9025f2bb 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84341a17..5b4ac227 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -214,7 +214,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex a40cb689..19da6da7 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 76d91c40..1af62530 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -211,7 +211,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png Binary files differindex 9e6bd786..b0b854bb 100644 --- a/docs/reference/SFO.solution-1.png +++ b/docs/reference/SFO.solution-1.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 2eb3a9b0..483869c4 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -188,7 +188,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png Binary files differindex 6739fe6b..cd58caec 100644 --- a/docs/reference/SFORB.solution-1.png +++ b/docs/reference/SFORB.solution-1.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index f2743fe4..b49700f8 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -205,7 +205,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 61f00d9b..fb369053 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex 2fab0ee4..df843300 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 06f877c2..298f2ebd 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 63aa358c..4ce43f9f 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -253,7 +253,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 5f419781..c180dce2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -66,7 +66,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -194,7 +194,7 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </div> <div class="pkgdown"> - 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Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do not imply a license to use them in the context of + pesticide registrations, as the use of the data may be constrained by + data protection regulations. +Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below. +Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues. +Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation. +Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16). +Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup. +Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR. +Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81)." /> +<meta name="twitter:card" content="summary" /> + + + +<!-- mathjax --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <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> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</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"> + <h1>Experimental datasets used for development and testing of error models</h1> + + <div class="hidden name"><code>experimental_data_for_UBA.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do not imply a license to use them in the context of + pesticide registrations, as the use of the data may be constrained by + data protection regulations.</p> +<p>Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below.</p> +<p>Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues.</p> +<p>Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation.</p> +<p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16).</p> +<p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup.</p> +<p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Germany, 2013b, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR.</p> +<p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81).</p> + + </div> + + <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, + each containing, among others, the following components</p><dl class='dl-horizontal'> + <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> + <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> + </dl> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + + <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> +<p>FOCUS (2014) “Generic guidance for Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Version 1.1, 18 December 2014 + <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> +<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate + and Behaviour</p> +<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the + environment</p> +<p>Ranke (2019) Documentation of results obtained for the error model expertise + written for the German Umweltbundesamt.</p> +<p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed + Decision of the United Kingdom made to the European Commission under Regulation (EC) No. + 1141/2010 for renewal of an active substance</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='co'># Model definitions</span> +<span class='no'>sfo_sfo</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</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'>dfop_sfo</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</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'>sfo_sfo_sfo</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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>A2</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'>dfop_sfo_sfo</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'>"DFOP"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>A2</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'>d_1_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>1</span>:<span class='fl'>2</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_1_2</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Soil"</span>, <span class='fl'>1</span>:<span class='fl'>2</span>) + + +<span class='no'>f_1_2_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"DFOP-SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>dfop_sfo_sfo</span>), <span class='no'>d_1_2</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>) + +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_1_2_tc</span>, <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> +</div> + </footer> + </div> + + + + </body> +</html> + diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 908aa8cc..286b40d4 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -174,7 +174,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 0a18d535..3eac2872 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -196,7 +196,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 42028d60..c5ac0d72 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -195,6 +195,12 @@ </tr><tr> <td> + <p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p> + </td> + <td><p>Function to plot squared residuals and the error model for an mkin object</p></td> + </tr><tr> + + <td> <p><code><a href="endpoints.html">endpoints()</a></code> </p> </td> <td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td> @@ -307,6 +313,12 @@ </tr><tr> <td> + <p><code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> </p> + </td> + <td><p>Experimental datasets used for development and testing of error models</p></td> + </tr><tr> + + <td> <p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p> </td> <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> @@ -529,7 +541,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 0184d573..a6cf4867 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -69,7 +69,7 @@ The total number of estimated parameters returned with the value </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -205,7 +205,7 @@ The total number of estimated parameters returned with the value </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png Binary files differindex 0aaa520b..b9fb891c 100644 --- a/docs/reference/logistic.solution-1.png +++ b/docs/reference/logistic.solution-1.png diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex d1831a46..752fd9d4 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 3b45b14f..cee169d2 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -242,7 +242,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 33c5ee4f..ad19853d 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -67,7 +67,7 @@ guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -196,7 +196,7 @@ guidance.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 859f315a..b9a42571 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 1db9a9d9..1af77f6b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -237,7 +237,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 7d0ad2fc..6f0d5376 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -208,7 +208,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 4fc0e2ed..869c4586 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -186,7 +186,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 2c01be70..89f40abf 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -176,7 +176,7 @@ in order to be compatible with mkinfit</p></dd> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 3ebea1e4..8fd09215 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -64,7 +64,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -211,7 +211,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 9c663646..476edc49 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 66da40b5..a0201963 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -68,7 +68,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -238,7 +238,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index bfca44fc..700b6805 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ Per default, parameters in the kinetic models are internally transformed in </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -163,6 +163,8 @@ Per default, parameters in the kinetic models are internally transformed in <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), + <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>), + <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> @@ -322,6 +324,41 @@ Per default, parameters in the kinetic models are internally transformed in distribution as assumed by this method.</p></td> </tr> <tr> + <th>error_model_algorithm</th> + <td><p>If the error model is "const", the error model algorithm is ignored, + because no special algorithm is needed and unweighted (also known as + ordinary) least squares fitting can be applied.</p> +<p>The default algorithm "d_3" will directly minimize the negative + log-likelihood and - independently - also use the three step algorithm + described below. The fit with the higher likelihood is returned.</p> +<p>The algorithm "direct" will directly minimize the negative + log-likelihood.</p> +<p>The algorithm "twostep" will minimize the negative log-likelihood + after an initial unweighted leas squares optimisation step.</p> +<p>The algorithm "threestep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, and then minimizes the negative log-likelihood + with free degradation and error model parameters.</p> +<p>The algorithm "fourstep" starts with unweighted least squares, + then optimizes only the error model using the degradation model + parameters found, then optimizes the degradation model again + with fixed error model parameters, and finally minimizes the negative + log-likelihood with free degradation and error model parameters.</p> +<p>The algorithm "IRLS" starts with unweighted least squares, + and then iterates optimization of the error model parameters and subsequent + optimization of the degradation model using those error model parameters, + until the error model parameters converge.</p></td> + </tr> + <tr> + <th>reweight.tol</th> + <td><p>Tolerance for the convergence criterion calculated from the error model + parameters in IRLS fits.</p></td> + </tr> + <tr> + <th>reweight.max.iter</th> + <td><p>Maximum number of iterations in IRLS fits.</p></td> + </tr> + <tr> <th>trace_parms</th> <td><p>Should a trace of the parameter values be listed?</p></td> </tr> @@ -360,20 +397,21 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed May 8 20:50:50 2019 -#> Date of summary: Wed May 8 20:50:50 2019 +#> Date of fit: Wed Jun 5 15:08:20 2019 +#> Date of summary: Wed Jun 5 15:08:20 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.456 s +#> Fitted using 222 model solutions performed in 0.469 s +#> +#> Error model: Constant variance #> -#> Error model: -#> Constant variance +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -443,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in <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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.488 0.000 1.488 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 +#> 1.579 0.000 1.581 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 #> @@ -515,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.086 0.000 1.087 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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 +#> 1.159 0.000 1.160 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -545,10 +583,10 @@ Per default, parameters in the kinetic models are internally transformed in <span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> </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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 + <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>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed May 8 20:51:06 2019 -#> Date of summary: Wed May 8 20:51:06 2019 +#> Date of fit: Wed Jun 5 15:08:36 2019 +#> Date of summary: Wed Jun 5 15:08:36 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -556,10 +594,11 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.082 s +#> Fitted using 421 model solutions performed in 1.181 s +#> +#> Error model: Constant variance #> -#> Error model: -#> Constant variance +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -663,10 +702,10 @@ Per default, parameters in the kinetic models are internally transformed in #> 100 m1 31.04 31.98163 -9.416e-01 #> 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.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed May 8 20:51:08 2019 -#> Date of summary: Wed May 8 20:51:08 2019 +#> Date of fit: Wed Jun 5 15:08:39 2019 +#> Date of summary: Wed Jun 5 15:08:39 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -674,19 +713,21 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 758 model solutions performed in 1.971 s +#> Fitted using 979 model solutions performed in 2.672 s #> -#> Error model: -#> Variance unique to each observed variable +#> Error model: Variance unique to each observed variable +#> +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> sigma_parent 3.0000 error -#> sigma_m1 3.0000 error +#> value type +#> parent_0 100.750000 state +#> k_parent 0.100000 deparm +#> k_m1 0.100100 deparm +#> f_parent_to_m1 0.500000 deparm +#> sigma_parent 3.398909 error +#> sigma_m1 2.857157 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper @@ -694,8 +735,8 @@ Per default, parameters in the kinetic models are internally transformed in #> log_k_parent -2.302585 -Inf Inf #> log_k_m1 -2.301586 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_parent 3.000000 0 Inf -#> sigma_m1 3.000000 0 Inf +#> sigma_parent 3.398909 0 Inf +#> sigma_m1 2.857157 0 Inf #> #> Fixed parameter values: #> value type @@ -715,14 +756,14 @@ Per default, parameters in the kinetic models are internally transformed in #> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670 #> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833 #> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158 -#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041368 +#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369 #> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000 -#> sigma_m1 -0.03385 -0.06627 0.02482 0.03925 -0.004628 +#> sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628 #> sigma_m1 #> parent_0 -0.033847 #> log_k_parent -0.066265 -#> log_k_m1 0.024821 -#> f_parent_ilr_1 0.039255 +#> log_k_m1 0.024823 +#> f_parent_ilr_1 0.039256 #> sigma_parent -0.004628 #> sigma_m1 1.000000 #> @@ -786,17 +827,17 @@ Per default, parameters in the kinetic models are internally transformed in #> 21 m1 46.44 41.65115 4.789e+00 #> 35 m1 41.22 43.29465 -2.075e+00 #> 35 m1 37.95 43.29465 -5.345e+00 -#> 50 m1 41.19 41.19948 -9.481e-03 +#> 50 m1 41.19 41.19948 -9.479e-03 #> 50 m1 40.01 41.19948 -1.189e+00 -#> 75 m1 40.09 36.44036 3.650e+00 -#> 75 m1 33.85 36.44036 -2.590e+00 -#> 100 m1 31.04 31.98774 -9.477e-01 -#> 100 m1 33.13 31.98774 1.142e+00 -#> 120 m1 25.15 28.80430 -3.654e+00 -#> 120 m1 33.31 28.80430 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.4 +#> 75 m1 40.09 36.44035 3.650e+00 +#> 75 m1 33.85 36.44035 -2.590e+00 +#> 100 m1 31.04 31.98773 -9.477e-01 +#> 100 m1 33.13 31.98773 1.142e+00 +#> 120 m1 25.15 28.80429 -3.654e+00 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed May 8 20:51:11 2019 -#> Date of summary: Wed May 8 20:51:11 2019 +#> Date of fit: Wed Jun 5 15:08:50 2019 +#> Date of summary: Wed Jun 5 15:08:50 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -804,28 +845,30 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 821 model solutions performed in 3.29 s +#> Fitted using 2289 model solutions performed in 10.959 s +#> +#> Error model: Two-component variance function #> -#> Error model: -#> Two-component variance function +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> sigma_low 0.1000 error -#> rsd_high 0.1000 error +#> value type +#> parent_0 1.007500e+02 state +#> k_parent 1.000000e-01 deparm +#> k_m1 1.001000e-01 deparm +#> f_parent_to_m1 5.000000e-01 deparm +#> sigma_low 5.641148e-03 error +#> rsd_high 8.430766e-02 error #> #> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_low 0.100000 0 Inf -#> rsd_high 0.100000 0 Inf +#> value lower upper +#> parent_0 100.750000000 -Inf Inf +#> log_k_parent -2.302585093 -Inf Inf +#> log_k_m1 -2.301585593 -Inf Inf +#> f_parent_ilr_1 0.000000000 -Inf Inf +#> sigma_low 0.005641148 0 Inf +#> rsd_high 0.084307660 0 Inf #> #> Fixed parameter values: #> value type @@ -856,7 +899,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Estimate t value Pr(>t) Lower Upper #> parent_0 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02 #> k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01 -#> k_m1 5.167e-03 10.9500 1.172e-12 0.004290 6.223e-03 +#> k_m1 5.167e-03 10.9500 1.171e-12 0.004290 6.223e-03 #> f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01 #> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02 #> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02 @@ -879,18 +922,18 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73433 -1.274329 -#> 0 parent 102.04 100.73433 1.305671 -#> 1 parent 93.50 91.09750 2.402495 -#> 1 parent 92.50 91.09750 1.402495 -#> 3 parent 63.23 74.50140 -11.271403 -#> 3 parent 68.99 74.50140 -5.511403 -#> 7 parent 52.32 49.82880 2.491205 -#> 7 parent 55.13 49.82880 5.301205 -#> 14 parent 27.27 24.64809 2.621909 -#> 14 parent 26.64 24.64809 1.991909 -#> 21 parent 11.50 12.19231 -0.692315 -#> 21 parent 11.64 12.19231 -0.552315 +#> 0 parent 99.46 100.73434 -1.274339 +#> 0 parent 102.04 100.73434 1.305661 +#> 1 parent 93.50 91.09751 2.402486 +#> 1 parent 92.50 91.09751 1.402486 +#> 3 parent 63.23 74.50141 -11.271410 +#> 3 parent 68.99 74.50141 -5.511410 +#> 7 parent 52.32 49.82880 2.491201 +#> 7 parent 55.13 49.82880 5.301201 +#> 14 parent 27.27 24.64809 2.621908 +#> 14 parent 26.64 24.64809 1.991908 +#> 21 parent 11.50 12.19232 -0.692315 +#> 21 parent 11.64 12.19232 -0.552315 #> 35 parent 2.85 2.98327 -0.133266 #> 35 parent 2.91 2.98327 -0.073266 #> 50 parent 0.69 0.66013 0.029874 @@ -899,24 +942,24 @@ Per default, parameters in the kinetic models are internally transformed in #> 75 parent 0.06 0.05344 0.006562 #> 1 m1 4.84 4.88645 -0.046451 #> 1 m1 5.64 4.88645 0.753549 -#> 3 m1 12.91 13.22867 -0.318668 -#> 3 m1 12.96 13.22867 -0.268668 -#> 7 m1 22.97 25.36416 -2.394164 -#> 7 m1 24.47 25.36416 -0.894164 -#> 14 m1 41.69 37.00974 4.680265 -#> 14 m1 33.21 37.00974 -3.799735 -#> 21 m1 44.37 41.90133 2.468670 -#> 21 m1 46.44 41.90133 4.538670 -#> 35 m1 41.22 43.45691 -2.236914 -#> 35 m1 37.95 43.45691 -5.506914 -#> 50 m1 41.19 41.34199 -0.151988 -#> 50 m1 40.01 41.34199 -1.331988 -#> 75 m1 40.09 36.61471 3.475290 -#> 75 m1 33.85 36.61471 -2.764710 -#> 100 m1 31.04 32.20083 -1.160830 -#> 100 m1 33.13 32.20083 0.929170 -#> 120 m1 25.15 29.04131 -3.891312 -#> 120 m1 33.31 29.04131 4.268688</div><div class='input'> +#> 3 m1 12.91 13.22867 -0.318669 +#> 3 m1 12.96 13.22867 -0.268669 +#> 7 m1 22.97 25.36417 -2.394166 +#> 7 m1 24.47 25.36417 -0.894166 +#> 14 m1 41.69 37.00974 4.680263 +#> 14 m1 33.21 37.00974 -3.799737 +#> 21 m1 44.37 41.90133 2.468669 +#> 21 m1 46.44 41.90133 4.538669 +#> 35 m1 41.22 43.45691 -2.236913 +#> 35 m1 37.95 43.45691 -5.506913 +#> 50 m1 41.19 41.34199 -0.151985 +#> 50 m1 40.01 41.34199 -1.331985 +#> 75 m1 40.09 36.61471 3.475295 +#> 75 m1 33.85 36.61471 -2.764705 +#> 100 m1 31.04 32.20082 -1.160823 +#> 100 m1 33.13 32.20082 0.929177 +#> 120 m1 25.15 29.04130 -3.891304 +#> 120 m1 33.31 29.04130 4.268696</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -946,7 +989,7 @@ Per default, parameters in the kinetic models are internally transformed in </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 51be5465..ddab656c 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -68,7 +68,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -234,7 +234,7 @@ 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 file4bbd307f8763.c 2> file4bbd307f8763.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file50a55c3108b2.c 2> file50a55c3108b2.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: @@ -291,7 +291,7 @@ For the definition of model types and their parameters, the equations given </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 65918d53..d4259579 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 8cfb9374..71fd6245 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -177,7 +177,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 0c8ee269..5ac632c8 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -172,7 +172,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 8e2e307b..7e71ec27 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -328,17 +328,17 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.003 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( +#> 0.003 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.021 0.000 0.021 </div><div class='input'> +#> 0.022 0.000 0.022 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> <span class='no'>f</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_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 #> Sum of squared residuals at call 3: 552.5739 @@ -397,7 +397,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 344561de..d29181c3 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index ab3b35b4..45722db4 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -224,7 +224,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index b87ceca4..4d81f639 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -203,7 +203,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 9d86a2df..328cec9b 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 59d293d5..5e264309 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex a947ac65..0a58a86b 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 89048ea3..9d8c0931 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 0c81649c..29206932 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 3e297eb3..61a029fc 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -194,8 +194,8 @@ <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 -#> 0.048 0.024 5.085 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.074 0.004 19.089 </div><div class='input'> +#> 0.038 0.050 6.779 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 27.209 0.004 27.278 </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 #> 0.7340481 0.2659519 0.7505684 0.2494316 @@ -240,7 +240,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex bcf5d12c..9025f2bb 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index a9ee2f76..e0c3c0e2 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -244,7 +244,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex f70e9e31..0fe3c263 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 6facce0f..84bec348 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex b53b3134..557046da 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 70a936ee..60203c3d 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 2e208996..36fcff6a 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex 1da876b4..ad2ffa8c 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 7bfc17f6..5cab42fd 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -68,7 +68,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -269,9 +269,9 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> -<span class='co'># parent to sink included</span> -<span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), + <pre class="examples"><div class='input'># One parent compound, one metabolite, both single first order, path from +# parent to sink included +</div><div class='input'><span class='no'>SFO_SFO</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'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</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'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</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</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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_errplot</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><div class='input'> @@ -306,7 +306,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex 03d334f7..8cf969c9 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 25ed01cc..45d67b55 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 7f32afe2..47cd7eec 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex b03dffb2..44037bb4 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 3037ca24..0b626d1b 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -67,7 +67,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -197,8 +197,8 @@ If the current plot device is a tikz device, <pre class="examples"><div class='input'> </div><div class='input'> <span class='co'># Only use one core not to offend CRAN checks</span> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>) - <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> + <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='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> +#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span> <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> <span class='co'># generated by pkgdown, as far as I know).</span> @@ -227,7 +227,7 @@ If the current plot device is a tikz device, </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 1aa4485a..fdc6e0ac 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -187,7 +187,7 @@ plot(x, legend = FALSE, main = "auto", …)</pre> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 2cc112aa..7c401533 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -165,7 +165,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index d09b629e..4ca7631b 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -186,7 +186,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html index 28847afe..10afb77d 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/print.nafta.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -177,7 +177,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex 49967dc9..34356613 100644 --- a/docs/reference/schaefer07_complex_case-1.png +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 09f6d1e2..50e07d37 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -65,7 +65,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -216,7 +216,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 265c7d1f..b73b81f4 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -68,7 +68,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -195,7 +195,7 @@ This is the error model used for example by Werner et al. (1978). The model </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b3151da1..68b36542 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -209,20 +209,21 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.49.4 + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed May 8 20:52:12 2019 -#> Date of summary: Wed May 8 20:52:12 2019 +#> Date of fit: Wed Jun 5 15:10:34 2019 +#> Date of summary: Wed Jun 5 15:10:34 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.266 s +#> Fitted using 131 model solutions performed in 0.268 s #> -#> Error model: -#> Constant variance +#> Error model: Constant variance +#> +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -307,7 +308,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 2c2623e4..4a7ca728 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -40,7 +40,7 @@ Variance component 'a' is based on a normal distribution with standard deviation Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 for the increase of the standard deviation with y. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the measured values approximates lognormal distribution for high values, whereas we are using normally distributed error components all along. Initial concentrations for metabolites and all values where adding the variance component resulted @@ -78,7 +78,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -151,7 +151,7 @@ Compare also the code in the example section to see the degradation models." /> Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 for the increase of the standard deviation with y. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the measured values approximates lognormal distribution for high values, whereas we are using normally distributed error components all along.</p> <p>Initial concentrations for metabolites and all values where adding the variance component resulted @@ -253,7 +253,8 @@ add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789) return(d_NA) } -# The following is the two-component model of Rocke and Lorenzato (1995) +# The following is the simplified version of the two-component model of Rocke +# and Lorenzato (1995) sdfunc_twocomp = function(value, sd_low, rsd_high) { sqrt(sd_low^2 + value^2 * rsd_high^2) } @@ -304,7 +305,7 @@ summary(fit) </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex a9aeea21..fc05f896 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex f6c91bff..b0dfdd5a 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index bc988340..e40d320f 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -64,7 +64,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -231,7 +231,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 7e05480e..bf134334 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -71,7 +71,7 @@ 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="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> @@ -293,7 +293,7 @@ The transformation of sets of formation fractions is fragile, as it supposes </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p> </div> </footer> </div> |
