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diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index fecbe3b1..411341b8 100644
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<title>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance • mkin</title>
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+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet">
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<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span>
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@@ -74,7 +74,14 @@
<a href="../../news/index.html">News</a>
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-<ul class="nav navbar-nav navbar-right"></ul>
+<ul class="nav navbar-nav navbar-right">
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+ <span class="fab fa fab fa-github fa-lg"></span>
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@@ -87,12 +94,12 @@
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
- <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
+ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-11-01</h4>
-
+ <h4 class="date">2020-05-12</h4>
+ <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.Rmd"><code>vignettes/web_only/NAFTA_examples.Rmd</code></a></small>
<div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
</div>
@@ -112,12 +119,12 @@
<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" title="1">p5a &lt;-<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"><html><body><pre class="r"><span class="no">p5a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5a"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p5a)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5a</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p5a)</a></code></pre></div>
+<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5a</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 465.21753 56.27506 32.06401
@@ -143,7 +150,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 9.99e+01 1.41e-26 98.8116 101.0810
## k1 2.67e-02 5.05e-06 0.0243 0.0295
-## k2 2.86e-12 5.00e-01 0.0000 Inf
+## k2 2.17e-12 5.00e-01 0.0000 Inf
## g 6.47e-01 3.67e-06 0.6248 0.6677
## sigma 1.27e+00 8.91e-06 0.8395 1.6929
##
@@ -152,7 +159,7 @@
## DT50 DT90 DT50_rep
## SFO 67.7 2.25e+02 6.77e+01
## IORE 58.2 1.07e+03 3.22e+02
-## DFOP 55.5 4.42e+11 2.42e+11
+## DFOP 55.5 5.83e+11 3.20e+11
##
## Representative half-life:
## [1] 321.51</code></pre>
@@ -160,12 +167,12 @@
<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" title="1">p5b &lt;-<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="cb7"><html><body><pre class="r"><span class="no">p5b</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5b"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p5b)</a></code></pre></div>
+<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5b</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p5b)</a></code></pre></div>
+<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5b</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 94.81123 10.10936 7.55871
@@ -191,7 +198,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 9.84e+01 1.24e-27 97.8078 98.9187
## k1 1.55e-02 4.10e-04 0.0143 0.0167
-## k2 1.16e-11 5.00e-01 0.0000 Inf
+## k2 1.04e-11 5.00e-01 0.0000 Inf
## g 6.89e-01 2.92e-03 0.6626 0.7142
## sigma 6.48e-01 2.38e-05 0.4147 0.8813
##
@@ -200,7 +207,7 @@
## DT50 DT90 DT50_rep
## SFO 86.6 2.88e+02 8.66e+01
## IORE 85.5 7.17e+02 2.16e+02
-## DFOP 83.6 9.80e+10 5.98e+10
+## DFOP 83.6 1.09e+11 6.67e+10
##
## Representative half-life:
## [1] 215.87</code></pre>
@@ -208,12 +215,12 @@
<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" title="1">p6 &lt;-<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="cb13"><html><body><pre class="r"><span class="no">p6</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p6"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p6)</a></code></pre></div>
+<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p6</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p6)</a></code></pre></div>
+<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p6</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 188.45361 51.00699 42.46931
@@ -239,7 +246,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 9.66e+01 1.57e-25 95.3476 97.8979
## k1 2.55e-02 7.33e-06 0.0233 0.0278
-## k2 4.90e-11 5.00e-01 0.0000 Inf
+## k2 3.88e-11 5.00e-01 0.0000 Inf
## g 8.61e-01 7.55e-06 0.8314 0.8867
## sigma 1.46e+00 6.93e-06 0.9661 1.9483
##
@@ -248,7 +255,7 @@
## DT50 DT90 DT50_rep
## SFO 38.6 1.28e+02 3.86e+01
## IORE 34.0 1.77e+02 5.32e+01
-## DFOP 34.1 6.66e+09 1.41e+10
+## DFOP 34.1 8.42e+09 1.79e+10
##
## Representative half-life:
## [1] 53.17</code></pre>
@@ -256,12 +263,12 @@
<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" title="1">p7 &lt;-<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="cb19"><html><body><pre class="r"><span class="no">p7</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p7"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p7)</a></code></pre></div>
+<div class="sourceCode" id="cb22"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p7</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p7)</a></code></pre></div>
+<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p7</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 3661.661 3195.030 3174.145
@@ -287,7 +294,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 9.89e+01 9.44e-49 95.4640 102.2573
## k1 1.81e-02 1.75e-01 0.0116 0.0281
-## k2 1.97e-10 5.00e-01 0.0000 Inf
+## k2 2.30e-10 5.00e-01 0.0000 Inf
## g 6.06e-01 2.19e-01 0.4826 0.7178
## sigma 7.40e+00 2.97e-15 6.0201 8.7754
##
@@ -296,7 +303,7 @@
## DT50 DT90 DT50_rep
## SFO 94.3 3.13e+02 9.43e+01
## IORE 96.7 1.51e+03 4.55e+02
-## DFOP 96.4 6.97e+09 3.52e+09
+## DFOP 96.4 5.95e+09 3.01e+09
##
## Representative half-life:
## [1] 454.55</code></pre>
@@ -309,12 +316,12 @@
<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" title="1">p8 &lt;-<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://rdrr.io/r/base/c.html">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="cb25"><html><body><pre class="r"><span class="no">p8</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p8"</span>]], <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">k__iore_parent_sink</span> <span class="kw">=</span> <span class="fl">1e-3</span>))</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p8)</a></code></pre></div>
+<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p8</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p8)</a></code></pre></div>
+<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p8</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 1996.9408 444.9237 547.5616
@@ -361,12 +368,12 @@
<div id="example-on-page-9-upper-panel" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2>
-<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">p9a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="no">p9a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9a"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9a)</a></code></pre></div>
+<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9a</span>)</pre></body></html></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" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p9a)</a></code></pre></div>
+<div class="sourceCode" id="cb35"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9a</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 839.35238 88.57064 9.93363
@@ -392,7 +399,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 9.85e+01 2.54e-20 97.390 99.672
## k1 1.38e-01 3.52e-05 0.131 0.146
-## k2 6.02e-13 5.00e-01 0.000 Inf
+## k2 6.69e-13 5.00e-01 0.000 Inf
## g 6.52e-01 8.13e-06 0.642 0.661
## sigma 7.88e-01 6.13e-02 0.481 1.095
##
@@ -401,7 +408,7 @@
## DT50 DT90 DT50_rep
## SFO 16.9 5.63e+01 1.69e+01
## IORE 11.6 3.37e+02 1.01e+02
-## DFOP 10.5 2.07e+12 1.15e+12
+## DFOP 10.5 1.86e+12 1.04e+12
##
## Representative half-life:
## [1] 101.43</code></pre>
@@ -410,17 +417,12 @@
<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" title="1">p9b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<div class="sourceCode" id="cb37"><html><body><pre class="r"><span class="no">p9b</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9b"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9b)</a></code></pre></div>
+<div class="sourceCode" id="cb40"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9b</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p9b)</a></code></pre></div>
+<div class="sourceCode" id="cb41"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9b</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 35.64867 23.22334 35.64867
@@ -447,7 +449,7 @@
## parent_0 94.7123 1.61e-16 93.1355 96.2891
## k1 0.0389 1.43e-06 0.0312 0.0485
## k2 0.0389 6.67e-03 0.0186 0.0812
-## g 0.7742 NaN NA NA
+## g 0.7742 5.00e-01 0.0000 1.0000
## sigma 1.5957 2.50e-04 0.9135 2.2779
##
##
@@ -464,12 +466,12 @@
<div id="example-on-page-10" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2>
-<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1">p10 &lt;-<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="cb43"><html><body><pre class="r"><span class="no">p10</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p10"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p10)</a></code></pre></div>
+<div class="sourceCode" id="cb46"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p10</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
-<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p10)</a></code></pre></div>
+<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p10</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 899.4089 336.4348 899.4089
@@ -492,12 +494,12 @@
## sigma 4.90 1.77e-04 2.837 6.968
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1 0.0495 6.42e-04 0.0301 0.0814
-## k2 0.0495 1.66e-02 0.0200 0.1225
-## g 0.6634 5.00e-01 0.0000 1.0000
-## sigma 8.0152 2.50e-04 4.5886 11.4418
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.810
+## k1 0.0495 6.48e-04 0.0303 0.081
+## k2 0.0495 1.67e-02 0.0201 0.122
+## g 0.6634 5.00e-01 0.0000 1.000
+## sigma 8.0152 2.50e-04 4.5886 11.442
##
##
## DTx values:
@@ -517,12 +519,12 @@
<div id="example-on-page-11" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2>
-<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1">p11 &lt;-<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="cb49"><html><body><pre class="r"><span class="no">p11</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p11"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p11)</a></code></pre></div>
+<div class="sourceCode" id="cb52"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p11</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p11)</a></code></pre></div>
+<div class="sourceCode" id="cb53"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p11</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 579.6805 204.7932 144.7783
@@ -560,7 +562,7 @@
## DFOP 4.21e+11 2.64e+12 9.56e+11
##
## Representative half-life:
-## [1] 41148169</code></pre>
+## [1] 41148171</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>
@@ -571,14 +573,14 @@
<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="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">p12a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div>
-<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no
-## covariance matrix</code></pre>
+<div class="sourceCode" id="cb55"><html><body><pre class="r"><span class="no">p12a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12a"</span>]])</pre></body></html></div>
+<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
+## matrix</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12a)</a></code></pre></div>
+<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12a</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
-<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p12a)</a></code></pre></div>
+<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12a</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 695.4440 220.0685 695.4440
@@ -603,8 +605,8 @@
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
## parent_0 100.521 2.74e-10 92.2366 108.805
-## k1 0.124 5.74e-06 0.0958 0.161
-## k2 0.124 6.61e-02 0.0319 0.484
+## k1 0.124 5.75e-06 0.0958 0.161
+## k2 0.124 6.72e-02 0.0319 0.484
## g 0.877 5.00e-01 0.0000 1.000
## sigma 7.048 2.50e-04 4.0349 10.061
##
@@ -621,20 +623,20 @@
<div id="example-on-page-12-lower-panel" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2>
-<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1">p12b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb62"><html><body><pre class="r"><span class="no">p12b</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12b"</span>]])</pre></body></html></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12b)</a></code></pre></div>
+<div class="sourceCode" id="cb72"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12b</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
-<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p12b)</a></code></pre></div>
+<div class="sourceCode" id="cb73"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12b</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 58.90242 19.06353 58.90242
@@ -677,16 +679,12 @@
<div id="example-on-page-13" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2>
-<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<div class="sourceCode" id="cb75"><html><body><pre class="r"><span class="no">p13</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p13)</a></code></pre></div>
+<div class="sourceCode" id="cb78"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p13</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
-<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p13)</a></code></pre></div>
+<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p13</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 174.5971 142.3951 174.5971
@@ -711,9 +709,9 @@
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01
-## k1 0.00258 4.28e-01 1.70e-08 3.92e+02
+## k1 0.00258 4.28e-01 1.45e-08 4.61e+02
## k2 0.00258 3.69e-08 2.20e-03 3.03e-03
-## g 0.00442 5.00e-01 NA NA
+## g 0.00442 5.00e-01 0.00e+00 1.00e+00
## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00
##
##
@@ -730,16 +728,16 @@
<div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1">
<h1 class="hasAnchor">
<a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1>
-<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb81"><html><body><pre class="r"><span class="no">p14</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p14)</a></code></pre></div>
+<div class="sourceCode" id="cb87"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p14</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
-<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p14)</a></code></pre></div>
+<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p14</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 48.43249 28.67746 27.26248
@@ -765,7 +763,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
## k1 9.53e-03 1.20e-01 0.00638 0.0143
-## k2 7.29e-12 5.00e-01 0.00000 Inf
+## k2 7.70e-12 5.00e-01 0.00000 Inf
## g 3.98e-01 2.19e-01 0.30481 0.4998
## sigma 1.17e+00 7.68e-06 0.77406 1.5610
##
@@ -774,7 +772,7 @@
## DT50 DT90 DT50_rep
## SFO 2.48e+02 8.25e+02 2.48e+02
## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 2.54e+10 2.46e+11 9.51e+10
+## DFOP 2.41e+10 2.33e+11 9.00e+10
##
## Representative half-life:
## [1] 6697.44</code></pre>
@@ -783,17 +781,16 @@
<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="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1">p15a &lt;-<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="cb90"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<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://rdrr.io/r/graphics/plot.html">plot</a></span>(p15a)</a></code></pre></div>
+<div class="sourceCode" id="cb96"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15a</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
-<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p15a)</a></code></pre></div>
+<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15a</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 245.5248 135.0132 245.5248
@@ -816,12 +813,12 @@
## sigma 3.105 1.78e-04 1.795 4.416
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 97.96752 2.85e-13 94.21914 101.7159
-## k1 0.00952 6.80e-02 0.00277 0.0327
-## k2 0.00952 3.82e-06 0.00902 0.0100
-## g 0.17247 NaN NA NA
-## sigma 4.18778 2.50e-04 2.39747 5.9781
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 97.96752 NA 94.21914 101.7159
+## k1 0.00952 NA 0.00241 0.0377
+## k2 0.00952 NA 0.00747 0.0121
+## g 0.17247 NA NA NA
+## sigma 4.18778 NA 2.39747 5.9781
##
##
## DTx values:
@@ -832,16 +829,16 @@
##
## Representative half-life:
## [1] 41.33</code></pre>
-<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb99"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite
-## result is doubtful</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15b)</a></code></pre></div>
+<div class="sourceCode" id="cb105"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15b</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
-<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p15b)</a></code></pre></div>
+<div class="sourceCode" id="cb106"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15b</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 106.91629 68.55574 106.91629
@@ -858,18 +855,18 @@
##
## $IORE
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 99.83 1.81e-16 97.51349 102.14
+## parent_0 99.83 1.81e-16 97.51348 102.14
## k__iore_parent_sink 0.38 3.22e-01 0.00352 41.05
-## N_parent 0.00 5.00e-01 -1.07695 1.08
+## N_parent 0.00 5.00e-01 -1.07696 1.08
## sigma 2.21 2.57e-04 1.23245 3.19
##
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 1.01e+02 NA 9.82e+01 1.04e+02
-## k1 4.86e-03 NA 6.75e-04 3.49e-02
-## k2 4.86e-03 NA 3.37e-03 6.99e-03
+## parent_0 1.01e+02 NA 98.24464 1.04e+02
+## k1 4.86e-03 NA 0.00068 3.47e-02
+## k2 4.86e-03 NA 0.00338 6.99e-03
## g 1.50e-01 NA NA NA
-## sigma 2.76e+00 NA 1.58e+00 3.94e+00
+## sigma 2.76e+00 NA 1.58208 3.94e+00
##
##
## DTx values:
@@ -885,14 +882,14 @@
<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="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" title="1">p16 &lt;-<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="cb108"><html><body><pre class="r"><span class="no">p16</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p16"</span>]])</pre></body></html></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="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p16)</a></code></pre></div>
+<div class="sourceCode" id="cb113"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p16</span>)</pre></body></html></div>
<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
-<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p16)</a></code></pre></div>
+<div class="sourceCode" id="cb114"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p16</span>)</pre></body></html></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 3831.804 2062.008 1550.980
@@ -917,7 +914,7 @@
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
## parent_0 88.5333 7.40e-18 79.9836 97.083
-## k1 18.5561 5.00e-01 0.0000 Inf
+## k1 18.5560 5.00e-01 0.0000 Inf
## k2 0.0776 1.41e-05 0.0518 0.116
## g 0.4733 1.41e-09 0.3674 0.582
## sigma 7.1902 2.11e-08 5.2785 9.102
@@ -950,53 +947,11 @@
</div>
</div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <div id="tocnav">
- <h2 class="hasAnchor">
-<a href="#tocnav" class="anchor"></a>Contents</h2>
- <ul class="nav nav-pills nav-stacked">
-<li><a href="#introduction">Introduction</a></li>
- <li>
-<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#example-on-page-5-upper-panel">Example on page 5, upper panel</a></li>
- <li><a href="#example-on-page-5-lower-panel">Example on page 5, lower panel</a></li>
- <li><a href="#example-on-page-6">Example on page 6</a></li>
- <li><a href="#example-on-page-7">Example on page 7</a></li>
- </ul>
-</li>
- <li>
-<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#example-on-page-8">Example on page 8</a></li>
- </ul>
-</li>
- <li>
-<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#example-on-page-9-upper-panel">Example on page 9, upper panel</a></li>
- <li><a href="#example-on-page-9-lower-panel">Example on page 9, lower panel</a></li>
- <li><a href="#example-on-page-10">Example on page 10</a></li>
- </ul>
-</li>
- <li>
-<a href="#the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#example-on-page-11">Example on page 11</a></li>
- </ul>
-</li>
- <li>
-<a href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate constant</a><ul class="nav nav-pills nav-stacked">
-<li><a href="#example-on-page-12-upper-panel">Example on page 12, upper panel</a></li>
- <li><a href="#example-on-page-12-lower-panel">Example on page 12, lower panel</a></li>
- <li><a href="#example-on-page-13">Example on page 13</a></li>
- </ul>
-</li>
- <li><a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF</a></li>
- <li><a href="#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></li>
- <li><a href="#the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1</a></li>
- <li><a href="#conclusions">Conclusions</a></li>
- <li><a href="#references">References</a></li>
- </ul>
+ <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
+ </nav>
</div>
- </div>
</div>
@@ -1007,7 +962,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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