diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-03-02 18:03:54 +0100 |
| commit | 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch) | |
| tree | f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/articles/web_only/NAFTA_examples.html | |
| parent | 351248d07f810ccb6c497633a02cd48ee35526e6 (diff) | |
Make tests more platform independent, update docs
Diffstat (limited to 'docs/articles/web_only/NAFTA_examples.html')
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 1569 |
1 files changed, 789 insertions, 780 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 65a71b56..996e5d49 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -19,6 +19,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -31,7 +33,7 @@ </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">1.0.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> </span> </div> @@ -57,6 +59,9 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> @@ -79,7 +84,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -94,908 +99,908 @@ - </header><script src="NAFTA_examples_files/header-attrs-2.7/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">26 February 2019 (rebuilt 2021-03-31)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-03-02)</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> </div> -<div id="introduction" class="section level1"> -<h1 class="hasAnchor"> -<a href="#introduction" class="anchor"></a>Introduction</h1> +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> <p>In this document, the example evaluations provided in Attachment 1 to the SOP of US EPA for using the NAFTA guidance <span class="citation">(US EPA 2015)</span> are repeated using mkin. The original evaluations reported in the attachment were performed using PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version distributed at the US EPA website today (2019-02-26).</p> <p>The datasets are now distributed with the mkin package.</p> </div> -<div id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="anchor"></a>Examples where DFOP did not converge with PestDF 0.8.4</h1> +<div class="section level2"> +<h2 id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4<a class="anchor" aria-label="anchor" href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4"></a> +</h2> <p>In attachment 1, it is reported that the DFOP model does not converge for these datasets when PestDF 0.8.4 was used. For all four datasets, the DFOP model can be fitted with mkin (see below). The negative half-life given by PestDF 0.8.4 for these fits appears to be the result of a bug. The results for the other two models (SFO and IORE) are the same.</p> -<div id="example-on-page-5-upper-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> +<div class="section level3"> +<h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a> +</h3> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 465.21753 56.27506 32.06401 -## -## Critical sum of squares for checking the SFO model: -## [1] 64.4304 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 4.67e-21 92.245 99.4357 -## k_parent 0.0102 3.92e-12 0.009 0.0117 -## sigma 4.8230 3.81e-06 3.214 6.4318 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 -## N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -## sigma 1.68e+00 NA 1.12e+00 2.24e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 -## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.26e-12 5.00e-01 0.0000 Inf -## g 6.47e-01 3.67e-06 0.6248 0.6677 -## sigma 1.27e+00 8.91e-06 0.8395 1.6929 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 67.7 2.25e+02 6.77e+01 -## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.59e+11 3.07e+11 -## -## Representative half-life: -## [1] 321.51</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 465.21753 56.27506 32.06401 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 64.4304</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span> +<span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span> +<span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> +<span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> +<span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> +<span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> +<span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span> +<span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span> +<span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 67.7 2.25e+02 6.77e+01</span> +<span class="co">## IORE 58.2 1.07e+03 3.22e+02</span> +<span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 321.51</span></code></pre> </div> -<div id="example-on-page-5-lower-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> +<div class="section level3"> +<h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a> +</h3> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 94.81123 10.10936 7.55871 -## -## Critical sum of squares for checking the SFO model: -## [1] 11.77879 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497 2.32e-24 94.85271 98.14155 -## k_parent 0.008 3.42e-14 0.00737 0.00869 -## sigma 2.295 1.22e-05 1.47976 3.11036 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 -## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04 -## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00 -## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 -## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 8.63e-12 5.00e-01 0.0000 Inf -## g 6.89e-01 2.92e-03 0.6626 0.7142 -## sigma 6.48e-01 2.38e-05 0.4147 0.8813 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 86.6 2.88e+02 8.66e+01 -## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.32e+11 8.04e+10 -## -## Representative half-life: -## [1] 215.87</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 94.81123 10.10936 7.55871 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 11.77879</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span> +<span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span> +<span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span> +<span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span> +<span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span> +<span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span> +<span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span> +<span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span> +<span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span> +<span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 86.6 2.88e+02 8.66e+01</span> +<span class="co">## IORE 85.5 7.17e+02 2.16e+02</span> +<span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 215.87</span></code></pre> </div> -<div id="example-on-page-6" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> +<div class="section level3"> +<h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a> +</h3> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 188.45361 51.00699 42.46931 -## -## Critical sum of squares for checking the SFO model: -## [1] 58.39888 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 7.29e-24 92.3478 97.2039 -## k_parent 0.0179 8.02e-16 0.0166 0.0194 -## sigma 3.0696 3.81e-06 2.0456 4.0936 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 97.12446 2.63e-26 95.62461 98.62431 -## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472 -## N_parent 1.49587 4.07e-13 1.33896 1.65279 -## sigma 1.59698 5.05e-06 1.06169 2.13227 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 -## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.22e-11 5.00e-01 0.0000 Inf -## g 8.61e-01 7.55e-06 0.8314 0.8867 -## sigma 1.46e+00 6.93e-06 0.9661 1.9483 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 38.6 1.28e+02 3.86e+01 -## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 1.01e+10 2.15e+10 -## -## Representative half-life: -## [1] 53.17</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 188.45361 51.00699 42.46931 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 58.39888</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span> +<span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span> +<span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span> +<span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span> +<span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span> +<span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span> +<span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span> +<span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span> +<span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span> +<span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 38.6 1.28e+02 3.86e+01</span> +<span class="co">## IORE 34.0 1.77e+02 5.32e+01</span> +<span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 53.17</span></code></pre> </div> -<div id="example-on-page-7" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> +<div class="section level3"> +<h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a> +</h3> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 3661.661 3195.030 3174.145 -## -## Critical sum of squares for checking the SFO model: -## [1] 3334.194 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 4.80e-53 93.32245 99.51347 -## k_parent 0.00735 7.64e-21 0.00641 0.00843 -## sigma 7.94557 1.83e-15 6.46713 9.42401 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 -## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03 -## N_parent 2.45e+00 NA 1.35e+00 3.54e+00 -## sigma 7.42e+00 NA 6.04e+00 8.80e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 -## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 3.63e-10 5.00e-01 0.0000 Inf -## g 6.06e-01 2.19e-01 0.4826 0.7178 -## sigma 7.40e+00 2.97e-15 6.0201 8.7754 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 94.3 3.13e+02 9.43e+01 -## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 3.77e+09 1.91e+09 -## -## Representative half-life: -## [1] 454.55</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 3661.661 3195.030 3174.145 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 3334.194</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span> +<span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span> +<span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span> +<span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span> +<span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span> +<span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span> +<span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span> +<span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span> +<span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span> +<span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 94.3 3.13e+02 9.43e+01</span> +<span class="co">## IORE 96.7 1.51e+03 4.55e+02</span> +<span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 454.55</span></code></pre> </div> </div> -<div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="anchor"></a>Examples where the representative half-life deviates from the observed DT50</h1> -<div id="example-on-page-8" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> +<div class="section level2"> +<h2 id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50<a class="anchor" aria-label="anchor" href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-8">Example on page 8<a class="anchor" aria-label="anchor" href="#example-on-page-8"></a> +</h3> <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="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></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> +<code class="sourceCode R"><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 1996.9408 444.9237 547.5616 -## -## Critical sum of squares for checking the SFO model: -## [1] 477.4924 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.16549 6.53e-29 83.37344 92.95754 -## k_parent 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 -## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 -## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04 -## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00 -## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 -## -## $DFOP -## 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: -## DT50 DT90 DT50_rep -## SFO 86.3 287 86.3 -## IORE 53.4 668 201.0 -## DFOP 55.6 517 253.0 -## -## Representative half-life: -## [1] 201.03</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 1996.9408 444.9237 547.5616 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 477.4924</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span> +<span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span> +<span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span> +<span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span> +<span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span> +<span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span> +<span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span> +<span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span> +<span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span> +<span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 86.3 287 86.3</span> +<span class="co">## IORE 53.4 668 201.0</span> +<span class="co">## DFOP 55.6 517 253.0</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 201.03</span></code></pre> </div> </div> -<div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study" class="anchor"></a>Examples where SFO was not selected for an abiotic study</h1> -<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="section level2"> +<h2 id="examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study<a class="anchor" aria-label="anchor" href="#examples-where-sfo-was-not-selected-for-an-abiotic-study"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a> +</h3> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> <div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 839.35238 88.57064 9.93363 -## -## Critical sum of squares for checking the SFO model: -## [1] 105.5678 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 3.06e-12 79.9447 96.4419 -## k_parent 0.0409 2.07e-07 0.0324 0.0516 -## sigma 7.2429 3.92e-05 4.4768 10.0090 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 -## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04 -## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00 -## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 2.54e-20 97.390 99.672 -## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.02e-13 5.00e-01 0.000 Inf -## g 6.52e-01 8.13e-06 0.642 0.661 -## sigma 7.88e-01 6.13e-02 0.481 1.095 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 16.9 5.63e+01 1.69e+01 -## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.69e+11 -## -## Representative half-life: -## [1] 101.43</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 839.35238 88.57064 9.93363 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 105.5678</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span> +<span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span> +<span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span> +<span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span> +<span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span> +<span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span> +<span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span> +<span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span> +<span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span> +<span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 16.9 5.63e+01 1.69e+01</span> +<span class="co">## IORE 11.6 3.37e+02 1.01e+02</span> +<span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 101.43</span></code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> -<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="section level3"> +<h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a> +</h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): 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> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 35.64867 23.22334 35.64867 -## -## Critical sum of squares for checking the SFO model: -## [1] 28.54188 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 2.15e-19 93.178 96.2464 -## k_parent 0.0389 4.47e-14 0.037 0.0408 -## sigma 1.5957 1.28e-04 0.932 2.2595 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 93.863 2.32e-18 92.4565 95.269 -## k__iore_parent 0.127 1.85e-02 0.0504 0.321 -## N_parent 0.711 1.88e-05 0.4843 0.937 -## sigma 1.288 1.76e-04 0.7456 1.830 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 1.61e-16 93.1355 96.2891 -## k1 0.0389 1.08e-04 0.0266 0.0569 -## k2 0.0389 2.23e-04 0.0255 0.0592 -## g 0.5256 NaN NA NA -## sigma 1.5957 2.50e-04 0.9135 2.2779 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 17.8 59.2 17.8 -## IORE 18.4 49.2 14.8 -## DFOP 17.8 59.2 17.8 -## -## Representative half-life: -## [1] 14.8</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 35.64867 23.22334 35.64867 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 28.54188</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span> +<span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span> +<span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span> +<span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span> +<span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span> +<span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span> +<span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span> +<span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span> +<span class="co">## g 0.5256 NaN NA NA</span> +<span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 17.8 59.2 17.8</span> +<span class="co">## IORE 18.4 49.2 14.8</span> +<span class="co">## DFOP 17.8 59.2 17.8</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 14.8</span></code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> -<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="section level3"> +<h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> +</h3> <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): 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> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 899.4089 336.4348 899.4089 -## -## Critical sum of squares for checking the SFO model: -## [1] 413.4841 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 6.42e-11 91.9259 111.5371 -## k_parent 0.0495 1.70e-07 0.0404 0.0607 -## sigma 8.0152 1.28e-04 4.6813 11.3491 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.86 3.32e-12 90.848 102.863 -## k__iore_parent 2.96 7.91e-02 0.687 12.761 -## N_parent 0.00 5.00e-01 -0.372 0.372 -## sigma 4.90 1.77e-04 2.837 6.968 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 1.41e-09 91.6534 111.8097 -## k1 0.0495 6.58e-03 0.0303 0.0809 -## k2 0.0495 2.60e-03 0.0410 0.0598 -## g 0.4487 5.00e-01 NA NA -## sigma 8.0152 2.50e-04 4.5886 11.4418 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 14.0 46.5 14.00 -## IORE 16.4 29.4 8.86 -## DFOP 14.0 46.5 14.00 -## -## Representative half-life: -## [1] 8.86</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 899.4089 336.4348 899.4089 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 413.4841</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span> +<span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span> +<span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span> +<span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span> +<span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span> +<span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span> +<span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span> +<span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span> +<span class="co">## g 0.4487 5.00e-01 NA NA</span> +<span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 14.0 46.5 14.00</span> +<span class="co">## IORE 16.4 29.4 8.86</span> +<span class="co">## DFOP 14.0 46.5 14.00</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 8.86</span></code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> -<div id="the-dt50-was-not-observed-during-the-study" class="section level1"> -<h1 class="hasAnchor"> -<a href="#the-dt50-was-not-observed-during-the-study" class="anchor"></a>The DT50 was not observed during the study</h1> -<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="section level2"> +<h2 id="the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study<a class="anchor" aria-label="anchor" href="#the-dt50-was-not-observed-during-the-study"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> +</h3> <div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 579.6805 204.7932 144.7783 -## -## Critical sum of squares for checking the SFO model: -## [1] 251.6944 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 -## k_parent 0.00321 4.71e-05 0.00222 4.64e-03 -## sigma 6.43473 1.28e-04 3.75822 9.11e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 -## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14 -## N_parent 8.36e+00 NA 6.62e+00 1.01e+01 -## sigma 3.82e+00 NA 2.21e+00 5.44e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 -## k1 4.41e-02 5.95e-03 0.0296 0.0658 -## k2 9.94e-13 5.00e-01 0.0000 Inf -## g 3.22e-01 1.45e-03 0.2814 0.3650 -## sigma 3.22e+00 3.52e-04 1.8410 4.5906 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 2.16e+02 7.18e+02 2.16e+02 -## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 3.07e+11 1.93e+12 6.98e+11 -## -## Representative half-life: -## [1] 41148170</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 579.6805 204.7932 144.7783 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 251.6944</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span> +<span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span> +<span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span> +<span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span> +<span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span> +<span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span> +<span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span> +<span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span> +<span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span> +<span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span> +<span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span> +<span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 41148170</span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> -<div id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="section level1"> -<h1 class="hasAnchor"> -<a href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="anchor"></a>N is less than 1 and the DFOP rate constants are like the SFO rate constant</h1> +<div class="section level2"> +<h2 id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate constant<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant"></a> +</h2> <p>In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.</p> -<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="section level3"> +<h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> +</h3> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance -## matrix</code></pre> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): 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> +<pre><code><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> +<span class="co">## matrix</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> <div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 695.4440 220.0685 695.4440 -## -## Critical sum of squares for checking the SFO model: -## [1] 270.4679 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 8.75e-12 92.461 108.581 -## k_parent 0.124 3.61e-08 0.104 0.148 -## sigma 7.048 1.28e-04 4.116 9.980 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.823 NA NA NA -## k__iore_parent 2.436 NA NA NA -## N_parent 0.263 NA NA NA -## sigma 3.965 NA NA NA -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 2.74e-10 92.2366 108.805 -## k1 0.124 2.53e-05 0.0908 0.170 -## k2 0.124 2.52e-02 0.0456 0.339 -## g 0.793 NaN NA NA -## sigma 7.048 2.50e-04 4.0349 10.061 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 5.58 18.5 5.58 -## IORE 6.49 13.2 3.99 -## DFOP 5.58 18.5 5.58 -## -## Representative half-life: -## [1] 3.99</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 695.4440 220.0685 695.4440 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 270.4679</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span> +<span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span> +<span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 96.823 NA NA NA</span> +<span class="co">## k__iore_parent 2.436 NA NA NA</span> +<span class="co">## N_parent 0.263 NA NA NA</span> +<span class="co">## sigma 3.965 NA NA NA</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span> +<span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span> +<span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span> +<span class="co">## g 0.793 NaN NA NA</span> +<span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 5.58 18.5 5.58</span> +<span class="co">## IORE 6.49 13.2 3.99</span> +<span class="co">## DFOP 5.58 18.5 5.58</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 3.99</span></code></pre> </div> -<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="section level3"> +<h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> +</h3> <div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</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> +<pre><code><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> <div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 58.90242 19.06353 58.90242 -## -## Critical sum of squares for checking the SFO model: -## [1] 51.51756 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 0.00039 85.9388 109.4292 -## k_parent 0.0589 0.00261 0.0431 0.0805 -## sigma 3.4323 0.04356 -1.2377 8.1023 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.523 0.0055 74.539157 116.51 -## k__iore_parent 0.333 0.1433 0.000717 154.57 -## N_parent 0.568 0.0677 -0.989464 2.13 -## sigma 1.953 0.0975 -5.893100 9.80 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NaN NaN NaN -## k1 0.0589 NaN NA NA -## k2 0.0589 NaN NA NA -## g 0.6473 NaN NA NA -## sigma 3.4323 NaN NaN NaN -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 11.8 39.1 11.80 -## IORE 12.9 31.4 9.46 -## DFOP 11.8 39.1 11.80 -## -## Representative half-life: -## [1] 9.46</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 58.90242 19.06353 58.90242 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 51.51756</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span> +<span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span> +<span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span> +<span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span> +<span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span> +<span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 97.6840 NaN NaN NaN</span> +<span class="co">## k1 0.0589 NaN NA NA</span> +<span class="co">## k2 0.0589 NaN NA NA</span> +<span class="co">## g 0.6473 NaN NA NA</span> +<span class="co">## sigma 3.4323 NaN NaN NaN</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 11.8 39.1 11.80</span> +<span class="co">## IORE 12.9 31.4 9.46</span> +<span class="co">## DFOP 11.8 39.1 11.80</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 9.46</span></code></pre> </div> -<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="section level3"> +<h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> +</h3> <div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> <div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 174.5971 142.3951 174.5971 -## -## Critical sum of squares for checking the SFO model: -## [1] 172.131 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 5.99e-17 89.61936 95.85065 -## k_parent 0.00258 2.42e-09 0.00223 0.00299 -## sigma 3.41172 7.07e-05 2.05455 4.76888 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.6016 6.34e-16 88.53086 94.672 -## k__iore_parent 0.0396 2.36e-01 0.00207 0.759 -## N_parent 0.3541 1.46e-01 -0.35153 1.060 -## sigma 3.0811 9.64e-05 1.84296 4.319 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA 8.95e+01 95.92118 -## k1 0.00258 NA 4.14e-04 0.01611 -## k2 0.00258 NA 1.74e-03 0.00383 -## g 0.16452 NA 0.00e+00 1.00000 -## sigma 3.41172 NA 2.02e+00 4.79960 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 269 892 269 -## IORE 261 560 169 -## DFOP 269 892 269 -## -## Representative half-life: -## [1] 168.51</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 174.5971 142.3951 174.5971 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 172.131</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span> +<span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span> +<span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span> +<span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span> +<span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span> +<span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span> +<span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span> +<span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span> +<span class="co">## g 0.16452 NA 0.00e+00 1.00000</span> +<span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 269 892 269</span> +<span class="co">## IORE 261 560 169</span> +<span class="co">## DFOP 269 892 269</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 168.51</span></code></pre> </div> </div> -<div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> -<h1 class="hasAnchor"> -<a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> +<div class="section level2"> +<h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> +</h2> <div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): 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> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> <div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 48.43249 28.67746 27.26248 -## -## Critical sum of squares for checking the SFO model: -## [1] 32.83337 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 -## k_parent 0.00279 3.75e-15 0.00256 3.04e-03 -## sigma 1.55616 3.81e-06 1.03704 2.08e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA NaN NaN -## k__iore_parent 9.44e-08 NA NaN NaN -## N_parent 3.31e+00 NA NaN NaN -## sigma 1.20e+00 NA 0.796 1.6 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 -## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 6.08e-12 5.00e-01 0.00000 Inf -## g 3.98e-01 2.19e-01 0.30481 0.4998 -## sigma 1.17e+00 7.68e-06 0.77406 1.5610 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 2.48e+02 8.25e+02 2.48e+02 -## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 3.05e+10 2.95e+11 1.14e+11 -## -## Representative half-life: -## [1] 6697.44</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 48.43249 28.67746 27.26248 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 32.83337</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span> +<span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span> +<span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.00e+02 NA NaN NaN</span> +<span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span> +<span class="co">## N_parent 3.31e+00 NA NaN NaN</span> +<span class="co">## sigma 1.20e+00 NA 0.796 1.6</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span> +<span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span> +<span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span> +<span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span> +<span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span> +<span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span> +<span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 6697.44</span></code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> -<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="section level2"> +<h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> +</h2> <div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> <div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 245.5248 135.0132 245.5248 -## -## Critical sum of squares for checking the SFO model: -## [1] 165.9335 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 2.00e-15 94.32049 101.615 -## k_parent 0.00952 4.93e-09 0.00824 0.011 -## sigma 4.18778 1.28e-04 2.44588 5.930 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.874 2.94e-15 92.937 98.811 -## k__iore_parent 0.629 2.11e-01 0.044 8.982 -## N_parent 0.000 5.00e-01 -0.642 0.642 -## sigma 3.105 1.78e-04 1.795 4.416 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 2.85e-13 94.21913 101.7159 -## k1 0.00952 6.28e-02 0.00250 0.0363 -## k2 0.00952 1.27e-04 0.00646 0.0140 -## g 0.21241 5.00e-01 0.00000 1.0000 -## sigma 4.18778 2.50e-04 2.39747 5.9781 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 72.8 242 72.8 -## IORE 76.3 137 41.3 -## DFOP 72.8 242 72.8 -## -## Representative half-life: -## [1] 41.33</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 245.5248 135.0132 245.5248 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 165.9335</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span> +<span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span> +<span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span> +<span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span> +<span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span> +<span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span> +<span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span> +<span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span> +<span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span> +<span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 72.8 242 72.8</span> +<span class="co">## IORE 76.3 137 41.3</span> +<span class="co">## DFOP 72.8 242 72.8</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 41.33</span></code></pre> <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): 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> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> <div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 106.91629 68.55574 106.91629 -## -## Critical sum of squares for checking the SFO model: -## [1] 84.25618 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 -## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03 -## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51349 102.14 -## k__iore_parent 0.38 3.22e-01 0.00352 41.05 -## N_parent 0.00 5.00e-01 -1.07696 1.08 -## sigma 2.21 2.57e-04 1.23245 3.19 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 -## k1 4.86e-03 NA 8.63e-04 2.73e-02 -## k2 4.86e-03 NA 3.21e-03 7.35e-03 -## g 1.88e-01 NA NA NA -## sigma 2.76e+00 NA 1.58e+00 3.94e+00 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 143 474 143.0 -## IORE 131 236 71.2 -## DFOP 143 474 143.0 -## -## Representative half-life: -## [1] 71.18</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 106.91629 68.55574 106.91629 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 84.25618</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span> +<span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span> +<span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span> +<span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span> +<span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span> +<span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span> +<span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span> +<span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span> +<span class="co">## g 1.88e-01 NA NA NA</span> +<span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 143 474 143.0</span> +<span class="co">## IORE 131 236 71.2</span> +<span class="co">## DFOP 143 474 143.0</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 71.18</span></code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> -<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="section level2"> +<h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> +</h2> <div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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> +<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> +<pre><code><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></code></pre> +<pre><code><span class="co">## to the terminal degradation rate found with the DFOP model.</span></code></pre> +<pre><code><span class="co">## The representative half-life obtained from the DFOP model may be used</span></code></pre> <div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> <div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 3831.804 2062.008 1550.980 -## -## Critical sum of squares for checking the SFO model: -## [1] 2247.348 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 2.33e-13 60.509 83.40 -## k_parent 0.159 4.86e-05 0.102 0.25 -## sigma 11.302 1.25e-08 8.308 14.30 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 -## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595 -## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046 -## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.8461 5.00e-01 0.0000 Inf -## k2 0.0776 1.41e-05 0.0518 0.116 -## g 0.4733 1.41e-09 0.3674 0.582 -## sigma 7.1902 2.11e-08 5.2785 9.102 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 4.35 14.4 4.35 -## IORE 1.48 32.1 9.67 -## DFOP 0.67 21.4 8.93 -## -## Representative half-life: -## [1] 8.93</code></pre> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Sums of squares:</span> +<span class="co">## SFO IORE DFOP </span> +<span class="co">## 3831.804 2062.008 1550.980 </span> +<span class="co">## </span> +<span class="co">## Critical sum of squares for checking the SFO model:</span> +<span class="co">## [1] 2247.348</span> +<span class="co">## </span> +<span class="co">## Parameters:</span> +<span class="co">## $SFO</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span> +<span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span> +<span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span> +<span class="co">## </span> +<span class="co">## $IORE</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span> +<span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span> +<span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span> +<span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span> +<span class="co">## </span> +<span class="co">## $DFOP</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span> +<span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span> +<span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span> +<span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span> +<span class="co">## </span> +<span class="co">## </span> +<span class="co">## DTx values:</span> +<span class="co">## DT50 DT90 DT50_rep</span> +<span class="co">## SFO 4.35 14.4 4.35</span> +<span class="co">## IORE 1.48 32.1 9.67</span> +<span class="co">## DFOP 0.67 21.4 8.93</span> +<span class="co">## </span> +<span class="co">## Representative half-life:</span> +<span class="co">## [1] 8.93</span></code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> -<div id="conclusions" class="section level1"> -<h1 class="hasAnchor"> -<a href="#conclusions" class="anchor"></a>Conclusions</h1> +<div class="section level2"> +<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> +</h2> <p>The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.</p> <p>Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.</p> </div> -<div id="references" class="section level1 unnumbered"> -<h1 class="hasAnchor"> -<a href="#references" class="anchor"></a>References</h1> +<div class="section level2"> +<h2 class="unnumbered" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> <div id="refs" class="references hanging-indent"> <div id="ref-usepa2015"> <p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p> @@ -1015,11 +1020,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> </footer> @@ -1028,5 +1035,7 @@ + + </body> </html> |