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1 files changed, 283 insertions, 250 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index cae0cd6b..db1fc478 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -88,7 +88,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -110,12 +110,14 @@ <div id="example-on-page-5-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -125,22 +127,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.84012168 1.095639e-21 92.120517864 99.55972549 -## k_parent_sink 0.01024015 1.710227e-12 0.008996874 0.01165524 +## Estimate Pr(>t) Lower Upper +## parent_0 95.8401 1.10e-21 92.121 99.5597 +## k_parent_sink 0.0102 1.71e-12 0.009 0.0117 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02 -## k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05 -## N_parent 2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 2.37e-26 9.89e+01 1.03e+02 +## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05 +## N_parent 2.57e+00 1.14e-11 2.22e+00 2.92e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.994630e+01 4.330861e-27 NA NA -## k1 2.674255e-02 3.171390e-05 NA NA -## k2 2.161318e-12 5.000000e-01 NA NA -## g 6.465276e-01 2.129114e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.99e+01 4.33e-27 NA NA +## k1 2.67e-02 3.17e-05 NA NA +## k2 2.16e-12 5.00e-01 NA NA +## g 6.47e-01 2.13e-05 NA NA ## ## ## DTx values: @@ -155,12 +157,14 @@ <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -170,22 +174,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497133849 2.623748e-25 94.776528606 98.217739092 -## k_parent_sink 0.008002704 1.352275e-14 0.007356108 0.008706135 +## Estimate Pr(>t) Lower Upper +## parent_0 96.497 2.62e-25 94.77653 98.21774 +## k_parent_sink 0.008 1.35e-14 0.00736 0.00871 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.854518e+01 1.019174e-29 9.780760e+01 9.928276e+01 -## k__iore_parent_sink 1.532766e-04 1.152046e-02 6.603390e-05 3.557826e-04 -## N_parent 1.939125e+00 8.177751e-13 1.741616e+00 2.136633e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 1.02e-29 9.78e+01 9.93e+01 +## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04 +## N_parent 1.94e+00 8.18e-13 1.74e+00 2.14e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.836323e+01 1.896304e-28 NA NA -## k1 1.546859e-02 2.833415e-03 NA NA -## k2 8.172408e-12 5.000000e-01 NA NA -## g 6.889941e-01 1.306276e-02 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.84e+01 1.90e-28 NA NA +## k1 1.55e-02 2.83e-03 NA NA +## k2 8.17e-12 5.00e-01 NA NA +## g 6.89e-01 1.31e-02 NA NA ## ## ## DTx values: @@ -200,12 +204,14 @@ <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -215,22 +221,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.77587412 1.246335e-24 92.25575879 97.29598945 -## k_parent_sink 0.01794259 2.347664e-16 0.01660595 0.01938682 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7759 1.25e-24 92.2558 97.2960 +## k_parent_sink 0.0179 2.35e-16 0.0166 0.0194 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 97.124460863 5.616271e-27 95.493434421 98.755487305 -## k__iore_parent_sink 0.002517728 3.535472e-03 0.001263771 0.005015906 -## N_parent 1.495871465 6.129227e-13 1.323799338 1.667943591 +## Estimate Pr(>t) Lower Upper +## parent_0 97.12446 5.62e-27 95.49343 98.75549 +## k__iore_parent_sink 0.00252 3.54e-03 0.00126 0.00502 +## N_parent 1.49587 6.13e-13 1.32380 1.66794 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.662275e+01 4.174516e-26 NA NA -## k1 2.547327e-02 2.115246e-05 NA NA -## k2 3.087623e-11 5.000000e-01 NA NA -## g 8.613785e-01 2.097173e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.66e+01 4.17e-26 NA NA +## k1 2.55e-02 2.12e-05 NA NA +## k2 3.09e-11 5.00e-01 NA NA +## g 8.61e-01 2.10e-05 NA NA ## ## ## DTx values: @@ -245,12 +251,14 @@ <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -260,22 +268,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.417960406 1.520951e-53 93.295541980 99.540378832 -## k_parent_sink 0.007350054 3.592731e-21 0.006413446 0.008423441 +## Estimate Pr(>t) Lower Upper +## parent_0 96.41796 1.52e-53 93.29554 99.54038 +## k_parent_sink 0.00735 3.59e-21 0.00641 0.00842 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.915322e+01 7.332574e-49 9.534934e+01 1.029571e+02 -## k__iore_parent_sink 1.600884e-05 3.472978e-01 9.982484e-08 2.567328e-03 -## N_parent 2.446000e+00 6.141482e-05 1.260173e+00 3.631827e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.92e+01 7.33e-49 9.53e+01 1.03e+02 +## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03 +## N_parent 2.45e+00 6.14e-05 1.26e+00 3.63e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.886065e+01 8.134302e-48 NA NA -## k1 1.805928e-02 2.198367e-01 NA NA -## k2 3.279731e-10 5.000000e-01 NA NA -## g 6.063177e-01 2.601365e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 8.13e-48 NA NA +## k1 1.81e-02 2.20e-01 NA NA +## k2 3.28e-10 5.00e-01 NA NA +## g 6.06e-01 2.60e-01 NA NA ## ## ## DTx values: @@ -295,12 +303,17 @@ <h2 class="hasAnchor"> <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system. + +## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -310,31 +323,31 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.165489334 NA NA NA -## k__iore_parent_sink 0.001000000 NA NA NA -## k_parent_sink 0.008032303 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 88.16549 NA NA NA +## k__iore_parent_sink 0.00100 NA NA NA +## k_parent_sink 0.00803 NA NA NA ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.771060e+01 1.048016e-35 9.442778e+01 1.009934e+02 -## k__iore_parent_sink 6.141041e-05 2.763666e-02 2.205805e-05 1.709688e-04 -## N_parent 2.271648e+00 5.996684e-19 2.015215e+00 2.528080e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.77e+01 1.05e-35 9.44e+01 1.01e+02 +## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04 +## N_parent 2.27e+00 6.00e-19 2.02e+00 2.53e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 95.706193520 NA NA NA -## k__iore_parent_sink 0.001000000 NA NA NA -## k1 0.024995243 NA NA NA -## k2 0.002734623 NA NA NA -## g 0.588349874 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.70619 NA NA NA +## k__iore_parent_sink 0.00100 NA NA NA +## k1 0.02500 NA NA NA +## k2 0.00273 NA NA NA +## g 0.58835 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 86.3 287 86.3 ## IORE 53.4 668 201.0 -## DFOP 55.6 517 253.0 +## DFOP 55.6 517 253.5 ## ## Representative half-life: ## [1] 201.0316</code></pre> @@ -346,12 +359,14 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -361,22 +376,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933161 1.117569e-12 79.76708923 96.61954288 -## k_parent_sink 0.0409019 9.501453e-08 0.03258829 0.05133639 +## Estimate Pr(>t) Lower Upper +## parent_0 88.1933 1.12e-12 79.7671 96.6195 +## k_parent_sink 0.0409 9.50e-08 0.0326 0.0513 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.891481e+01 5.163566e-17 9.497891e+01 1.028507e+02 -## k__iore_parent_sink 1.927824e-05 1.480158e-01 2.650455e-06 1.402214e-04 -## N_parent 2.910027e+00 3.738041e-09 2.428904e+00 3.391151e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 5.16e-17 9.50e+01 1.03e+02 +## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04 +## N_parent 2.91e+00 3.74e-09 2.43e+00 3.39e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.853112e+01 1.308505e-21 NA NA -## k1 1.382145e-01 3.630589e-09 NA NA -## k2 6.019228e-13 5.000000e-01 NA NA -## g 6.518659e-01 1.502543e-10 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 1.31e-21 NA NA +## k1 1.38e-01 3.63e-09 NA NA +## k2 6.02e-13 5.00e-01 NA NA +## g 6.52e-01 1.50e-10 NA NA ## ## ## DTx values: @@ -392,12 +407,14 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -407,22 +424,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.71226787 2.207090e-20 93.0673253 96.35721040 -## k_parent_sink 0.03887215 1.482921e-14 0.0368549 0.04099981 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 2.21e-20 93.0673 96.357 +## k_parent_sink 0.0389 1.48e-14 0.0369 0.041 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 93.8626223 2.911881e-19 92.29955547 95.4256890 -## k__iore_parent_sink 0.1271399 2.725876e-02 0.04570569 0.3536663 -## N_parent 0.7108771 3.130915e-05 0.46052920 0.9612249 +## Estimate Pr(>t) Lower Upper +## parent_0 93.863 2.91e-19 92.2996 95.426 +## k__iore_parent_sink 0.127 2.73e-02 0.0457 0.354 +## N_parent 0.711 3.13e-05 0.4605 0.961 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.71226786 NA NA NA -## k1 0.03887215 NA NA NA -## k2 0.03887215 NA NA NA -## g 0.77417779 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 NA NA NA +## k1 0.0389 NA NA NA +## k2 0.0389 NA NA NA +## g 0.7742 NA NA NA ## ## ## DTx values: @@ -438,12 +455,14 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -453,29 +472,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.73153064 4.954950e-11 90.96832870 112.49473259 -## k_parent_sink 0.04952864 3.398569e-07 0.03930194 0.06241642 +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 4.95e-11 90.9683 112.4947 +## k_parent_sink 0.0495 3.40e-07 0.0393 0.0624 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.855416 2.706118e-12 89.8843855 103.8264461 -## k__iore_parent_sink 2.960977 1.308097e-01 0.4609504 19.0202303 -## N_parent 0.000000 5.000000e-01 -0.4728922 0.4728922 +## Estimate Pr(>t) Lower Upper +## parent_0 96.86 2.71e-12 89.884 103.826 +## k__iore_parent_sink 2.96 1.31e-01 0.461 19.020 +## N_parent 0.00 5.00e-01 -0.473 0.473 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.73153022 NA NA NA -## k1 0.04952864 NA NA NA -## k2 0.04952864 NA NA NA -## g 0.66344649 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 NA NA NA +## k1 0.0495 NA NA NA +## k2 0.0495 NA NA NA +## g 0.6634 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 14.0 46.5 14.00 +## SFO 14.0 46.5 13.99 ## IORE 16.4 29.4 8.86 -## DFOP 14.0 46.5 14.00 +## DFOP 14.0 46.5 13.99 ## ## Representative half-life: ## [1] 8.862193</code></pre> @@ -488,12 +507,14 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -503,22 +524,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.158200840 1.560217e-13 89.913728706 1.024027e+02 -## k_parent_sink 0.003208498 5.266271e-05 0.002183575 4.714497e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 96.15820 1.56e-13 89.91373 1.02e+02 +## k_parent_sink 0.00321 5.27e-05 0.00218 4.71e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.045981e+02 NA 9.798102e+01 1.112151e+02 -## k__iore_parent_sink 3.110367e-17 NA 6.875825e-25 1.407014e-09 -## N_parent 8.360812e+00 NA 4.397006e+00 1.232462e+01 +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 NA 9.80e+01 1.11e+02 +## k__iore_parent_sink 3.11e-17 NA 6.88e-25 1.41e-09 +## N_parent 8.36e+00 NA 4.40e+00 1.23e+01 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.045607e+02 7.502642e-13 NA NA -## k1 4.414526e-02 3.343950e-02 NA NA -## k2 7.246905e-13 5.000000e-01 NA NA -## g 3.217737e-01 7.868540e-03 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 7.50e-13 NA NA +## k1 4.41e-02 3.34e-02 NA NA +## k2 7.25e-13 5.00e-01 NA NA +## g 3.22e-01 7.87e-03 NA NA ## ## ## DTx values: @@ -539,12 +560,14 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -554,22 +577,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.5206988 5.606929e-12 91.6867692 109.3546284 -## k_parent_sink 0.1243142 7.235485e-08 0.1017305 0.1519113 +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 5.61e-12 91.687 109.355 +## k_parent_sink 0.124 7.24e-08 0.102 0.152 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.8234045 1.242894e-13 91.56908085 102.0777281 -## k__iore_parent_sink 2.4360714 3.893118e-02 0.78536982 7.5562415 -## N_parent 0.2627157 3.639503e-02 -0.02875633 0.5541876 +## Estimate Pr(>t) Lower Upper +## parent_0 96.823 1.24e-13 91.5691 102.078 +## k__iore_parent_sink 2.436 3.89e-02 0.7854 7.556 +## N_parent 0.263 3.64e-02 -0.0288 0.554 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.5206988 NA NA NA -## k1 0.1243142 NA NA NA -## k2 0.1243142 NA NA NA -## g 0.8772377 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 NA NA NA +## k1 0.124 NA NA NA +## k2 0.124 NA NA NA +## g 0.877 NA NA NA ## ## ## DTx values: @@ -584,12 +607,14 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -599,29 +624,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840211 0.0000535970 86.32050115 109.04754103 -## k_parent_sink 0.0589177 0.0009869932 0.04320553 0.08034377 +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 5.36e-05 86.3205 109.0475 +## k_parent_sink 0.0589 9.87e-04 0.0432 0.0803 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.5232270 0.0003860431 84.09629121 106.950163 -## k__iore_parent_sink 0.3329365 0.1708863327 0.01026046 10.803285 -## N_parent 0.5677771 0.0548808046 -0.31606833 1.451622 +## Estimate Pr(>t) Lower Upper +## parent_0 95.523 0.000386 84.0963 106.95 +## k__iore_parent_sink 0.333 0.170886 0.0103 10.80 +## N_parent 0.568 0.054881 -0.3161 1.45 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840212 NA NA NA -## k1 0.0589177 NA NA NA -## k2 0.0589177 NA NA NA -## g 0.6901929 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 NA NA NA +## k1 0.0589 NA NA NA +## k2 0.0589 NA NA NA +## g 0.6902 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 11.8 39.1 11.80 +## SFO 11.8 39.1 11.76 ## IORE 12.9 31.4 9.46 -## DFOP 11.8 39.1 11.80 +## DFOP 11.8 39.1 11.76 ## ## Representative half-life: ## [1] 9.461912</code></pre> @@ -629,12 +654,14 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" data-line-number="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb70"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb70-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -644,22 +671,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.735003006 1.453426e-17 89.389064698 96.080941315 -## k_parent_sink 0.002581189 2.630396e-09 0.002198171 0.003030945 +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 1.45e-17 89.3891 96.08094 +## k_parent_sink 0.00258 2.63e-09 0.0022 0.00303 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.60158658 2.932498e-16 88.08710837 95.116065 -## k__iore_parent_sink 0.03960674 2.810573e-01 0.00102485 1.530656 -## N_parent 0.35408757 1.972378e-01 -0.51942545 1.227601 +## Estimate Pr(>t) Lower Upper +## parent_0 91.6016 2.93e-16 88.08711 95.12 +## k__iore_parent_sink 0.0396 2.81e-01 0.00102 1.53 +## N_parent 0.3541 1.97e-01 -0.51943 1.23 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.735003208 NA NA NA -## k1 0.002581186 NA NA NA -## k2 0.002581188 NA NA NA -## g 0.004422859 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 NA NA NA +## k1 0.00258 NA NA NA +## k2 0.00258 NA NA NA +## g 0.00442 NA NA NA ## ## ## DTx values: @@ -675,12 +702,14 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -690,22 +719,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.471243637 1.708290e-31 98.373131052 1.005694e+02 -## k_parent_sink 0.002789581 2.222078e-15 0.002554583 3.046197e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 99.47124 1.71e-31 98.37313 1.01e+02 +## k_parent_sink 0.00279 2.22e-15 0.00255 3.05e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.003522e+02 NA 9.926773e+01 1.014366e+02 -## k__iore_parent_sink 9.443770e-08 NA 6.810412e-11 1.309536e-04 -## N_parent 3.308552e+00 NA 1.690051e+00 4.927053e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 NA 9.93e+01 1.01e+02 +## k__iore_parent_sink 9.44e-08 NA 6.81e-11 1.31e-04 +## N_parent 3.31e+00 NA 1.69e+00 4.93e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.003398e+02 2.698790e-28 NA NA -## k1 9.532677e-03 3.394353e-01 NA NA -## k2 9.189935e-12 5.000000e-01 NA NA -## g 3.982564e-01 3.920847e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 2.70e-28 NA NA +## k1 9.53e-03 3.39e-01 NA NA +## k2 9.19e-12 5.00e-01 NA NA +## g 3.98e-01 3.92e-01 NA NA ## ## ## DTx values: @@ -721,12 +750,14 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -736,22 +767,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.967511635 4.984358e-16 94.038286642 101.8967366 -## k_parent_sink 0.009522227 5.239115e-09 0.008126698 0.0111574 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 4.98e-16 94.03829 101.8967 +## k_parent_sink 0.00952 5.24e-09 0.00813 0.0112 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.8736780 8.295860e-16 92.58018331 99.1671726 -## k__iore_parent_sink 0.6285106 2.386496e-01 0.03155477 12.5187302 -## N_parent 0.0000000 5.000000e-01 -0.72189225 0.7218923 +## Estimate Pr(>t) Lower Upper +## parent_0 95.874 8.30e-16 92.5802 99.167 +## k__iore_parent_sink 0.629 2.39e-01 0.0316 12.519 +## N_parent 0.000 5.00e-01 -0.7219 0.722 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.967516468 NA NA NA -## k1 0.009522243 NA NA NA -## k2 0.009522223 NA NA NA -## g 0.172466840 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 NA NA NA +## k1 0.00952 NA NA NA +## k2 0.00952 NA NA NA +## g 0.17247 NA NA NA ## ## ## DTx values: @@ -762,12 +793,14 @@ ## ## Representative half-life: ## [1] 41.32749</code></pre> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -777,29 +810,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.008816e+02 4.987925e-18 98.127607367 1.036355e+02 -## k_parent_sink 4.856586e-03 1.756208e-10 0.004316334 5.464459e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 4.99e-18 98.12761 1.04e+02 +## k_parent_sink 4.86e-03 1.76e-10 0.00432 5.46e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.8268283 4.490292e-17 97.19753163 102.45613 -## k__iore_parent_sink 0.3799625 3.406003e-01 0.00206198 70.01593 -## N_parent 0.0000000 5.000000e-01 -1.20105017 1.20105 +## Estimate Pr(>t) Lower Upper +## parent_0 99.83 4.49e-17 97.19753 102.5 +## k__iore_parent_sink 0.38 3.41e-01 0.00206 70.0 +## N_parent 0.00 5.00e-01 -1.20105 1.2 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.008816e+02 NA NA NA -## k1 4.856586e-03 NA NA NA -## k2 4.856586e-03 NA NA NA -## g 1.496838e-01 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA NA NA +## k1 4.86e-03 NA NA NA +## k2 4.86e-03 NA NA NA +## g 1.50e-01 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 143 474 143.0 +## SFO 143 474 142.7 ## IORE 131 236 71.2 -## DFOP 143 474 143.0 +## DFOP 143 474 142.7 ## ## Representative half-life: ## [1] 71.18014</code></pre> @@ -808,14 +841,14 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -825,22 +858,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.9528227 3.923531e-14 61.0870510 82.8185944 -## k_parent_sink 0.1594518 2.271601e-06 0.1110583 0.2289327 +## Estimate Pr(>t) Lower Upper +## parent_0 71.953 3.92e-14 61.087 82.819 +## k_parent_sink 0.159 2.27e-06 0.111 0.229 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 8.738846e+01 1.739390e-16 7.706991e+01 97.707005461 -## k__iore_parent_sink 4.549683e-04 2.282721e-01 3.008533e-05 0.006880303 -## N_parent 2.696278e+00 1.869479e-08 1.966442e+00 3.426114200 +## Estimate Pr(>t) Lower Upper +## parent_0 8.74e+01 1.74e-16 7.71e+01 97.70701 +## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05 0.00688 +## N_parent 2.70e+00 1.87e-08 1.97e+00 3.42611 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.53333334 NA 79.36733990 97.6993268 -## k1 18.55624337 NA 0.00000000 Inf -## k2 0.07759679 NA 0.04709945 0.1278414 -## g 0.47333008 NA 0.31375096 0.6385506 +## Estimate Pr(>t) Lower Upper +## parent_0 88.5333 NA 79.3673 97.699 +## k1 18.5562 NA 0.0000 Inf +## k2 0.0776 NA 0.0471 0.128 +## g 0.4733 NA 0.3138 0.639 ## ## ## DTx values: |