diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-26 21:12:21 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-02-26 21:12:21 +0100 |
| commit | 10f2314d12bc1e1664b1ff1db015d1df9f7fbe34 (patch) | |
| tree | d6d9cca6d8a394ccd4ff73a809cbd74806ec873f | |
| parent | 396e40d2c45d81a8e74c41a2f632665021e980a1 (diff) | |
Static documentation rebuilt by pkgdown
61 files changed, 264 insertions, 80 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml index 62dc7f07..e98469cd 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -35,6 +35,7 @@ reference: - FOCUS_2006_HS_ref_A_to_F - FOCUS_2006_DFOP_ref_A_to_B - NAFTA_SOP_2015 + - NAFTA_SOP_Attachment - mccall81_245T - schaefer07_complex_case - synthetic_data_for_UBA_2014 diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 9030710e..e01fd46d 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -64,6 +64,9 @@ <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> @@ -163,8 +166,8 @@ <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:04 2019 -## Date of summary: Tue Feb 26 20:25:04 2019 +## Date of fit: Tue Feb 26 21:09:15 2019 +## Date of summary: Tue Feb 26 21:09:15 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -172,7 +175,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.7 s +## Fitted with method Port using 153 model solutions performed in 0.712 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index a6853c97..aeded526 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -64,6 +64,9 @@ <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> @@ -111,15 +114,15 @@ <a class="sourceLine" id="cb2-2" data-line-number="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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:06 2019 -## Date of summary: Tue Feb 26 20:25:06 2019 +## Date of fit: Tue Feb 26 21:09:17 2019 +## Date of summary: Tue Feb 26 21:09:17 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.095 s +## Fitted with method Port using 37 model solutions performed in 0.096 s ## ## Weighting: none ## @@ -202,15 +205,15 @@ <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:08 2019 -## Date of summary: Tue Feb 26 20:25:08 2019 +## Date of fit: Tue Feb 26 21:09:19 2019 +## Date of summary: Tue Feb 26 21:09:19 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.509 s +## Fitted with method Port using 611 model solutions performed in 1.539 s ## ## Weighting: none ## @@ -297,15 +300,15 @@ <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:08 2019 -## Date of summary: Tue Feb 26 20:25:08 2019 +## Date of fit: Tue Feb 26 21:09:19 2019 +## Date of summary: Tue Feb 26 21:09:19 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.196 s +## Fitted with method Port using 81 model solutions performed in 0.199 s ## ## Weighting: none ## @@ -368,8 +371,8 @@ <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:09 2019 -## Date of summary: Tue Feb 26 20:25:09 2019 +## Date of fit: Tue Feb 26 21:09:20 2019 +## Date of summary: Tue Feb 26 21:09:20 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -378,7 +381,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.843 s +## Fitted with method Port using 336 model solutions performed in 0.844 s ## ## Weighting: none ## @@ -460,8 +463,8 @@ <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:10 2019 -## Date of summary: Tue Feb 26 20:25:11 2019 +## Date of fit: Tue Feb 26 21:09:21 2019 +## Date of summary: Tue Feb 26 21:09:22 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -561,8 +564,8 @@ <div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:11 2019 -## Date of summary: Tue Feb 26 20:25:11 2019 +## Date of fit: Tue Feb 26 21:09:22 2019 +## Date of summary: Tue Feb 26 21:09:22 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -621,8 +624,8 @@ <div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 20:25:11 2019 -## Date of summary: Tue Feb 26 20:25:11 2019 +## Date of fit: Tue Feb 26 21:09:22 2019 +## Date of summary: Tue Feb 26 21:09:22 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent diff --git a/docs/articles/index.html b/docs/articles/index.html index 49a501b7..9381dedb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -94,6 +94,9 @@ <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> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index f6e8af4d..d5d5e3bf 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -64,6 +64,9 @@ <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> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index c06672f1..af8dbd4e 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -64,6 +64,9 @@ <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> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index b398733b..1926662a 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -64,6 +64,9 @@ <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> diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index bd202a54..cae0cd6b 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -64,6 +64,9 @@ <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> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 0295d844..3d49d262 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -64,6 +64,9 @@ <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> @@ -126,9 +129,9 @@ <a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.318 1.000 2.317 0 -## 1 deSolve, not compiled 3 17.559 7.575 17.551 0 -## 2 Eigenvalue based 3 2.859 1.233 2.857 0 +## 3 deSolve, compiled 3 2.309 1.000 2.307 0 +## 1 deSolve, not compiled 3 17.535 7.594 17.527 0 +## 2 Eigenvalue based 3 2.846 1.233 2.844 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -157,8 +160,8 @@ <a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.093 1.000 4.090 0 -## 1 deSolve, not compiled 3 37.258 9.103 37.241 0 +## 2 deSolve, compiled 3 4.071 1.000 4.069 0 +## 1 deSolve, not compiled 3 37.139 9.123 37.123 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/news/index.html b/docs/news/index.html index a66f5bbc..c1644a00 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -94,6 +94,9 @@ <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> diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 2a4a6de4..1224fbe6 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 74e77339..38b8368c 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 40e2a0fa..378d6eb2 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index f10805a0..93be7412 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -97,6 +97,9 @@ <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> @@ -469,8 +472,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bb55ad0> -#> <environment: 0x55555c4dcf70> +#> <bytecode: 0x55555c80a350> +#> <environment: 0x55555b478bb8> #> #> $cost_notrans #> function (P) @@ -492,8 +495,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c537298> -#> <environment: 0x55555c4dcf70> +#> <bytecode: 0x55555c522e40> +#> <environment: 0x55555b478bb8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +563,7 @@ #> 99.17407 #> #> $date -#> [1] "Tue Feb 26 20:23:09 2019" +#> [1] "Tue Feb 26 21:07:19 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 9babae16..cdceeb0b 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -101,6 +101,9 @@ in this fit." /> <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> 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 6e11464e..0f51b1ce 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -101,6 +101,9 @@ in this fit." /> <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> 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 59219e45..e0b8d760 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -101,6 +101,9 @@ in this fit." /> <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> 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 67df3476..d07fb469 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -101,6 +101,9 @@ in this fit." /> <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> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 7d38639b..b766c88b 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 43466474..8763c878 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -101,6 +101,9 @@ The form given here differs slightly from the original reference by Gustafson <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> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 048a24c3..940d3186 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 9646461c..9a497f92 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index f4d89222..c8b97493 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 63b47855..373da052 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -97,6 +97,9 @@ <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> @@ -133,7 +136,7 @@ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - <p>Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable + <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index dd04ad1a..dea4527e 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 19566257..a09f3d94 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -101,6 +101,9 @@ <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> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 40f23bee..8b6668f1 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -99,6 +99,9 @@ <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> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index bd23c95a..4d777ce2 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -100,6 +100,9 @@ with the advantage that the SFORB model can also be used for metabolites." /> <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> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index e5a12b7d..f8beb987 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 0ab8f0a3..02c96b92 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/index.html b/docs/reference/index.html index 4e57fd3d..e1f149e2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -94,6 +94,9 @@ <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> @@ -280,6 +283,12 @@ </tr><tr> <td> + <p><code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> </p> + </td> + <td><p>Example datasets from Attachment 1 to the NAFTA SOP published 2015</p></td> + </tr><tr> + + <td> <p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p> </td> <td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 2f211431..229f8b04 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -114,6 +114,9 @@ In the case of iterative reweighting, the variances obtained by this <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> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index a30059fe..9687d7d3 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 17be80d5..f62ed5d5 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -101,6 +101,9 @@ guidance." /> <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> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 2e5f0ac2..bfb34489 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -99,6 +99,9 @@ <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> @@ -160,8 +163,8 @@ <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:32 2019 -#> Date of summary: Tue Feb 26 20:23:32 2019 +#> Date of fit: Tue Feb 26 21:07:42 2019 +#> Date of summary: Tue Feb 26 21:07:42 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +174,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.765 s +#> Fitted with method Port using 574 model solutions performed in 3.766 s #> #> Weighting: none #> @@ -249,8 +252,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:34 2019 -#> Date of summary: Tue Feb 26 20:23:34 2019 +#> Date of fit: Tue Feb 26 21:07:44 2019 +#> Date of summary: Tue Feb 26 21:07:44 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +263,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.601 s +#> Fitted with method Port using 246 model solutions performed in 1.612 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index f034f955..ee781c11 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -99,6 +99,9 @@ <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> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index e874f9bf..f2b9bef7 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index a9362c2b..3be872e8 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 149006a5..60769486 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -98,6 +98,9 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> <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> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 84c0fc49..2494faf9 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -107,6 +107,9 @@ <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> @@ -438,8 +441,8 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:36 2019 -#> Date of summary: Tue Feb 26 20:23:36 2019 +#> Date of fit: Tue Feb 26 21:07:47 2019 +#> Date of summary: Tue Feb 26 21:07:47 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -515,7 +518,7 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><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'>#> User System verstrichen -#> 1.081 0.000 1.081 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.111 0.000 1.112 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -590,7 +593,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.812 0.000 0.812 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.826 0.000 0.827 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -628,8 +631,8 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:48 2019 -#> Date of summary: Tue Feb 26 20:23:48 2019 +#> Date of fit: Tue Feb 26 21:07:59 2019 +#> Date of summary: Tue Feb 26 21:07:59 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -637,7 +640,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.852 s +#> Fitted with method Port using 186 model solutions performed in 0.841 s #> #> Weighting: none #> @@ -745,8 +748,8 @@ #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:51 2019 -#> Date of summary: Tue Feb 26 20:23:51 2019 +#> Date of fit: Tue Feb 26 21:08:02 2019 +#> Date of summary: Tue Feb 26 21:08:02 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -754,7 +757,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.6 s +#> Fitted with method Port using 551 model solutions performed in 2.596 s #> #> Weighting: none #> @@ -867,8 +870,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:52 2019 -#> Date of summary: Tue Feb 26 20:23:52 2019 +#> Date of fit: Tue Feb 26 21:08:03 2019 +#> Date of summary: Tue Feb 26 21:08:03 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -876,7 +879,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.704 s +#> Fitted with method Port using 155 model solutions performed in 0.701 s #> #> Weighting: mean #> @@ -985,8 +988,8 @@ <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'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:53 2019 -#> Date of summary: Tue Feb 26 20:23:53 2019 +#> Date of fit: Tue Feb 26 21:08:03 2019 +#> Date of summary: Tue Feb 26 21:08:03 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -994,7 +997,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.796 s +#> Fitted with method Port using 174 model solutions performed in 0.795 s #> #> Weighting: manual #> @@ -1105,8 +1108,8 @@ <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:54 2019 -#> Date of summary: Tue Feb 26 20:23:54 2019 +#> Date of fit: Tue Feb 26 21:08:05 2019 +#> Date of summary: Tue Feb 26 21:08:05 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1114,7 +1117,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.238 s +#> Fitted with method Port using 270 model solutions performed in 1.24 s #> #> Weighting: manual #> @@ -1223,8 +1226,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:23:58 2019 -#> Date of summary: Tue Feb 26 20:23:58 2019 +#> Date of fit: Tue Feb 26 21:08:08 2019 +#> Date of summary: Tue Feb 26 21:08:08 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1232,7 +1235,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.182 s +#> Fitted with method Port using 692 model solutions performed in 3.192 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index a6dd68c5..8c2ec38c 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -102,6 +102,9 @@ For the definition of model types and their parameters, the equations given <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> @@ -231,7 +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 file240f6aec3e43.c 2> file240f6aec3e43.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file3dbe7c3499b.c 2> file3dbe7c3499b.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f0706605..e819befe 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 2eed795a..573e8e7c 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index bab6deb8..fb4afa9a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -99,6 +99,9 @@ <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> @@ -325,7 +328,7 @@ <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 0.003 </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 @@ -335,7 +338,7 @@ <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 -#> 0.039 0.000 0.040 </div><div class='input'> +#> 0.039 0.000 0.039 </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'>#> Model cost at call 1 : 552.5739 #> Model cost at call 3 : 552.5739 diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index e1ba5acb..c216d8b8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -100,6 +100,9 @@ <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> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 3e0bdcbd..fee17102 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0078baed..44aaaa79 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -98,6 +98,9 @@ <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> @@ -191,8 +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 -#> 0.059 0.021 6.916 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 22.506 0.000 22.518 </div><div class='input'> +#> 0.041 0.032 6.955 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.625 0.004 22.646 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 9b879786..c05ce4cb 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -99,6 +99,9 @@ <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> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 44ac2967..7255b324 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -102,6 +102,9 @@ If the current plot device is a tikz device, <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> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index dd7b619d..e1651208 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -101,6 +101,9 @@ If the current plot device is a tikz device, <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> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 7949d36c..753cbd6a 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -101,6 +101,9 @@ <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> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 1d858500..96607b02 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index ace71925..7e138697 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -97,6 +97,9 @@ <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> diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html index 44f1f6e5..31bd2956 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/print.nafta.html @@ -99,6 +99,9 @@ <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> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index b7ba3d96..1e8a6d9e 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -99,6 +99,9 @@ <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> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index f44a1c14..eca5deec 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -102,6 +102,9 @@ This is the error model used for example by Werner et al. (1978). The model <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> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 6ec72f80..8d9e0287 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -100,6 +100,9 @@ <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> @@ -208,8 +211,8 @@ <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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:24:50 2019 -#> Date of summary: Tue Feb 26 20:24:50 2019 +#> Date of fit: Tue Feb 26 21:09:01 2019 +#> Date of summary: Tue Feb 26 21:09:01 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 6363db6f..6e36e72f 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -112,6 +112,9 @@ Compare also the code in the example section to see the degradation models." /> <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> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index b3ec4699..12904a1f 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -98,6 +98,9 @@ <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> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 6e65f609..115ee0ca 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -105,6 +105,9 @@ The transformation of sets of formation fractions is fragile, as it supposes <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> @@ -202,8 +205,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:24:58 2019 -#> Date of summary: Tue Feb 26 20:24:58 2019 +#> Date of fit: Tue Feb 26 21:09:09 2019 +#> Date of summary: Tue Feb 26 21:09:09 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -211,7 +214,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.707 s +#> Fitted with method Port using 153 model solutions performed in 0.709 s #> #> Weighting: none #> @@ -278,8 +281,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </div><div class='input'><span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:25:00 2019 -#> Date of summary: Tue Feb 26 20:25:00 2019 +#> Date of fit: Tue Feb 26 21:09:11 2019 +#> Date of summary: Tue Feb 26 21:09:11 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -287,7 +290,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.584 s +#> Fitted with method Port using 350 model solutions performed in 1.588 s #> #> Weighting: none #> @@ -366,8 +369,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:25:01 2019 -#> Date of summary: Tue Feb 26 20:25:01 2019 +#> Date of fit: Tue Feb 26 21:09:12 2019 +#> Date of summary: Tue Feb 26 21:09:12 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -375,7 +378,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.867 s +#> Fitted with method Port using 186 model solutions performed in 0.849 s #> #> Weighting: none #> @@ -450,8 +453,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 20:25:02 2019 -#> Date of summary: Tue Feb 26 20:25:02 2019 +#> Date of fit: Tue Feb 26 21:09:13 2019 +#> Date of summary: Tue Feb 26 21:09:13 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -459,7 +462,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.472 s +#> Fitted with method Port using 104 model solutions performed in 0.47 s #> #> Weighting: none #> diff --git a/man/NAFTA_SOP_Attachment.Rd b/man/NAFTA_SOP_Attachment.Rd index b8d015a4..cffb4bc6 100644 --- a/man/NAFTA_SOP_Attachment.Rd +++ b/man/NAFTA_SOP_Attachment.Rd @@ -9,7 +9,7 @@ Data taken from from Attachment 1 of the SOP. } \usage{NAFTA_SOP_Attachment} \format{ - Additionally, a list (NAFTA_SOP_Attachment) containing 16 datasets suitable + A list (NAFTA_SOP_Attachment) containing 16 datasets suitable for the evaluation with \code{\link{nafta}} } \source{ |