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1 files changed, 754 insertions, 744 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index df1e06db..b8ec5059 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +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">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-17)</h4> <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> @@ -128,205 +134,205 @@ <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><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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></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" 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 2.95e-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 4.28e+11 2.35e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 321.51</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 465.21753 56.27506 32.06401 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 64.4304</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span></span> +<span><span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span></span> +<span><span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span></span> +<span><span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span></span> +<span><span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> +<span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> +<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> +<span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> +<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> +<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 321.51</span></span></code></pre> </div> <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><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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></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" 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 9.41e-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 1.21e+11 7.36e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 215.87</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 94.81123 10.10936 7.55871 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 11.77879</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span></span> +<span><span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span></span> +<span><span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span> +<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span> +<span><span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span> +<span><span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> +<span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> +<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> +<span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> +<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> +<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 215.87</span></span></code></pre> </div> <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><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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></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" 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 4.40e-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 7.43e+09 1.58e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 53.17</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 188.45361 51.00699 42.46931 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 58.39888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span></span> +<span><span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span></span> +<span><span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span></span> +<span><span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span></span> +<span><span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span></span> +<span><span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> +<span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> +<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> +<span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> +<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> +<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 53.17</span></span></code></pre> </div> <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><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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></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" 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 2.81e-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 4.87e+09 2.46e+09</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 454.55</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3661.661 3195.030 3174.145 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 3334.194</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span> +<span><span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span></span> +<span><span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span></span> +<span><span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span></span> +<span><span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span></span> +<span><span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> +<span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> +<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> +<span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> +<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> +<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 454.55</span></span></code></pre> </div> </div> <div class="section level2"> @@ -337,52 +343,52 @@ </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" 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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></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" 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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 1996.9408 444.9237 547.5616 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 477.4924</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span> +<span><span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span></span> +<span><span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span> +<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span> +<span><span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span> +<span><span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span> +<span><span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span></span> +<span><span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span></span> +<span><span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span></span> +<span><span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.3 287 86.3</span></span> +<span><span class="co">## IORE 53.4 668 201.0</span></span> +<span><span class="co">## DFOP 55.6 517 253.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 201.03</span></span></code></pre> </div> </div> <div class="section level2"> @@ -392,160 +398,165 @@ <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><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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></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/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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></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" 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 7.68e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 101.43</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 839.35238 88.57064 9.93363 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 105.5678</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span></span> +<span><span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span></span> +<span><span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span> +<span><span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span> +<span><span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span> +<span><span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span></span> +<span><span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span></span> +<span><span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span></span> +<span><span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> +<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 101.43</span></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 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><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="cb40"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> -<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 2.24e-04 0.0255 0.0592</span> -<span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</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> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 35.64867 23.22334 35.64867 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 28.54188</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span></span> +<span><span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span></span> +<span><span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span></span> +<span><span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span></span> +<span><span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span></span> +<span><span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> +<span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> +<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 17.8 59.2 17.8</span></span> +<span><span class="co">## IORE 18.4 49.2 14.8</span></span> +<span><span class="co">## DFOP 17.8 59.2 17.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 14.8</span></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 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="cb43"><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><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="cb49"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<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 6.32e-03 0.0241 0.1018</span> -<span class="co">## k2 0.0495 2.41e-03 0.0272 0.0901</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> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 899.4089 336.4348 899.4089 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 413.4841</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span> +<span><span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span></span> +<span><span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span></span> +<span><span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span></span> +<span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> +<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> +<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> +<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 14.0 46.5 14.00</span></span> +<span><span class="co">## IORE 16.4 29.4 8.86</span></span> +<span><span class="co">## DFOP 14.0 46.5 14.00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.86</span></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> @@ -555,53 +566,53 @@ <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="cb52"><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><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="cb55"><pre class="downlit sourceCode r"> -<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="cb56"><pre class="downlit sourceCode r"> -<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 9.93e-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] 41148171</span></code></pre> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></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><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 579.6805 204.7932 144.7783 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 251.6944</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span> +<span><span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span></span> +<span><span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span></span> +<span><span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span></span> +<span><span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span></span> +<span><span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span></span> +<span><span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span></span> +<span><span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span></span> +<span><span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span></span> +<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span> +<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41148170</span></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> @@ -612,380 +623,379 @@ <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="cb58"><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><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> -<span class="co">## matrix</span> - -<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">## 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="cb62"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<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 NA NA NA</span> -<span class="co">## k1 0.124 NA NA NA</span> -<span class="co">## k2 0.124 NA NA NA</span> -<span class="co">## g 0.793 NA NA NA</span> -<span class="co">## sigma 7.048 NA NA NA</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 class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 695.4440 220.0685 695.4440 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 270.4679</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span></span> +<span><span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span></span> +<span><span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.823 NA NA NA</span></span> +<span><span class="co">## k__iore_parent 2.436 NA NA NA</span></span> +<span><span class="co">## N_parent 0.263 NA NA NA</span></span> +<span><span class="co">## sigma 3.965 NA NA NA</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> +<span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> +<span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> +<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 5.58 18.5 5.58</span></span> +<span><span class="co">## IORE 6.49 13.2 3.99</span></span> +<span><span class="co">## DFOP 5.58 18.5 5.58</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 3.99</span></span></code></pre> </div> <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="cb65"><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><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 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="cb71"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> -<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 class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 58.90242 19.06353 58.90242 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 51.51756</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span></span> +<span><span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span></span> +<span><span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span></span> +<span><span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span></span> +<span><span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span></span> +<span><span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 NaN NaN NaN</span></span> +<span><span class="co">## k1 0.0589 NaN NA NA</span></span> +<span><span class="co">## k2 0.0589 NaN NA NA</span></span> +<span><span class="co">## g 0.6473 NaN NA NA</span></span> +<span><span class="co">## sigma 3.4323 NaN NaN NaN</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 11.8 39.1 11.80</span></span> +<span><span class="co">## IORE 12.9 31.4 9.46</span></span> +<span><span class="co">## DFOP 11.8 39.1 11.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 9.46</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$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="cb80"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.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" 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 4.24e-04 0.01573</span> -<span class="co">## k2 0.00258 NA 1.76e-03 0.00379</span> -<span class="co">## g 0.16452 NA NA NA</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 class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 174.5971 142.3951 174.5971 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 172.131</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span> +<span><span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span></span> +<span><span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span></span> +<span><span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span></span> +<span><span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span></span> +<span><span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> +<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> +<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> +<span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 269 892 269</span></span> +<span><span class="co">## IORE 261 560 169</span></span> +<span><span class="co">## DFOP 269 892 269</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 168.51</span></span></code></pre> </div> </div> <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$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="cb89"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r"> -<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 5.03e-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 3.69e+10 3.57e+11 1.38e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 6697.44</span></code></pre> +<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 48.43249 28.67746 27.26248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 32.83337</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span> +<span><span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span></span> +<span><span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 NA NaN NaN</span></span> +<span><span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span></span> +<span><span class="co">## N_parent 3.31e+00 NA NaN NaN</span></span> +<span><span class="co">## sigma 1.20e+00 NA 0.796 1.6</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> +<span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> +<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> +<span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> +<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> +<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 6697.44</span></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 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="cb92"><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><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="cb98"><pre class="downlit sourceCode r"> -<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="cb99"><pre class="downlit sourceCode r"> -<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 0.00260 0.0349</span> -<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span> -<span class="co">## g 0.21241 5.00e-01 NA NA</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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb101"><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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></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><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 245.5248 135.0132 245.5248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 165.9335</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span> +<span><span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span></span> +<span><span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span></span> +<span><span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span></span> +<span><span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span></span> +<span><span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> +<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 72.8 242 72.8</span></span> +<span><span class="co">## IORE 76.3 137 41.3</span></span> +<span><span class="co">## DFOP 72.8 242 72.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41.33</span></span></code></pre> <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r"> -<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 -1.07695 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 8.62e-04 2.74e-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 0.00e+00 1.00e+00</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> +<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 106.91629 68.55574 106.91629 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 84.25618</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span> +<span><span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span></span> +<span><span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> +<span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> +<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> +<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 143 474 143.0</span></span> +<span><span class="co">## IORE 131 236 71.2</span></span> +<span><span class="co">## DFOP 143 474 143.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 71.18</span></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 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="cb107"><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><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="cb112"><pre class="downlit sourceCode r"> -<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="cb113"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> +<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> +<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></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><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></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3831.804 2062.008 1550.980 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 2247.348</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span></span> +<span><span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span></span> +<span><span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span></span> +<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span></span> +<span><span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span></span> +<span><span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span></span> +<span><span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span></span> +<span><span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span></span> +<span><span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 4.35 14.4 4.35</span></span> +<span><span class="co">## IORE 1.48 32.1 9.67</span></span> +<span><span class="co">## DFOP 0.67 21.4 8.93</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.93</span></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 class="section level2"> @@ -1022,7 +1032,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> |