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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /docs/articles/web_only/NAFTA_examples.html
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'docs/articles/web_only/NAFTA_examples.html')
-rw-r--r--docs/articles/web_only/NAFTA_examples.html322
1 files changed, 164 insertions, 158 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 411d4bb8..d3e23253 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -31,7 +31,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.0.0</span>
</span>
</div>
@@ -80,7 +80,7 @@
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin/">
- <span class="fab fa fab fa-github fa-lg"></span>
+ <span class="fab fa-github fa-lg"></span>
</a>
</li>
@@ -100,7 +100,7 @@
<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">2020-10-15</h4>
+ <h4 class="date">2021-02-03</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
<div class="hidden name"><code>NAFTA_examples.rmd</code></div>
@@ -122,15 +122,15 @@
<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="downlit">
-<span class="va">p5a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p5a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb4"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p>
-<div class="sourceCode" id="cb5"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 465.21753 56.27506 32.06401
@@ -156,7 +156,7 @@
## 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 2.17e-12 5.00e-01 0.0000 Inf
+## k2 2.42e-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
##
@@ -165,7 +165,7 @@
## 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 5.83e+11 3.20e+11
+## DFOP 55.5 5.22e+11 2.86e+11
##
## Representative half-life:
## [1] 321.51</code></pre>
@@ -173,15 +173,15 @@
<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="downlit">
-<span class="va">p5b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p5b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb10"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p>
-<div class="sourceCode" id="cb11"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 94.81123 10.10936 7.55871
@@ -207,7 +207,7 @@
## 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 1.04e-11 5.00e-01 0.0000 Inf
+## k2 1.10e-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
##
@@ -216,7 +216,7 @@
## 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 1.09e+11 6.67e+10
+## DFOP 83.6 1.03e+11 6.29e+10
##
## Representative half-life:
## [1] 215.87</code></pre>
@@ -224,15 +224,15 @@
<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="downlit">
-<span class="va">p6</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p6</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb16"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p>
-<div class="sourceCode" id="cb17"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 188.45361 51.00699 42.46931
@@ -258,7 +258,7 @@
## 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 3.88e-11 5.00e-01 0.0000 Inf
+## k2 3.60e-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
##
@@ -267,7 +267,7 @@
## 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 8.42e+09 1.79e+10
+## DFOP 34.1 9.07e+09 1.93e+10
##
## Representative half-life:
## [1] 53.17</code></pre>
@@ -275,15 +275,15 @@
<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="downlit">
-<span class="va">p7</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p7</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb22"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p>
-<div class="sourceCode" id="cb23"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 3661.661 3195.030 3174.145
@@ -309,7 +309,7 @@
## 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 2.30e-10 5.00e-01 0.0000 Inf
+## k2 2.89e-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
##
@@ -318,7 +318,7 @@
## 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 5.95e+09 3.01e+09
+## DFOP 96.4 4.75e+09 2.40e+09
##
## Representative half-life:
## [1] 454.55</code></pre>
@@ -331,15 +331,15 @@
<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="downlit">
-<span class="va">p8</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p8</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb28"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p>
-<div class="sourceCode" id="cb29"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 1996.9408 444.9237 547.5616
@@ -386,15 +386,15 @@
<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="downlit">
-<span class="va">p9a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p9a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb34"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p>
-<div class="sourceCode" id="cb35"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 839.35238 88.57064 9.93363
@@ -420,7 +420,7 @@
## 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 6.69e-13 5.00e-01 0.000 Inf
+## k2 9.03e-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
##
@@ -429,7 +429,7 @@
## 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 1.86e+12 1.04e+12
+## DFOP 10.5 1.38e+12 7.67e+11
##
## Representative half-life:
## [1] 101.43</code></pre>
@@ -438,15 +438,19 @@
<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="downlit">
-<span class="va">p9b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p9b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb40"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
-<div class="sourceCode" id="cb41"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 35.64867 23.22334 35.64867
@@ -469,12 +473,12 @@
## sigma 1.288 1.76e-04 0.7456 1.830
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## 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 5.00e-01 0.0000 1.0000
-## sigma 1.5957 2.50e-04 0.9135 2.2779
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 94.7123 NA 93.1355 96.2891
+## k1 0.0389 NA 0.0266 0.0569
+## k2 0.0389 NA 0.0255 0.0592
+## g 0.5256 NA NA NA
+## sigma 1.5957 NA 0.9135 2.2779
##
##
## DTx values:
@@ -490,15 +494,16 @@
<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="downlit">
-<span class="va">p10</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p10</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb46"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
-<div class="sourceCode" id="cb47"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb51"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 899.4089 336.4348 899.4089
@@ -521,12 +526,12 @@
## 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 111.810
-## 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
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.8097
+## k1 0.0495 5.63e-03 0.0240 0.1020
+## k2 0.0495 1.93e-03 0.0272 0.0903
+## g 0.4487 NaN 0.0000 1.0000
+## sigma 8.0152 2.50e-04 4.5886 11.4418
##
##
## DTx values:
@@ -546,15 +551,15 @@
<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="downlit">
-<span class="va">p11</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p11</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb52"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
-<div class="sourceCode" id="cb53"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 579.6805 204.7932 144.7783
@@ -580,7 +585,7 @@
## Estimate Pr(&gt;t) Lower Upper
## parent_0 1.05e+02 9.47e-13 99.9990 109.1224
## k1 4.41e-02 5.95e-03 0.0296 0.0658
-## k2 7.25e-13 5.00e-01 0.0000 Inf
+## k2 9.94e-13 5.00e-01 0.0000 Inf
## g 3.22e-01 1.45e-03 0.2814 0.3650
## sigma 3.22e+00 3.52e-04 1.8410 4.5906
##
@@ -589,7 +594,7 @@
## DT50 DT90 DT50_rep
## SFO 2.16e+02 7.18e+02 2.16e+02
## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 4.21e+11 2.64e+12 9.56e+11
+## DFOP 3.07e+11 1.93e+12 6.97e+11
##
## Representative half-life:
## [1] 41148171</code></pre>
@@ -603,17 +608,20 @@
<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="downlit">
-<span class="va">p12a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p12a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
+## matrix
+
+## 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="cb59"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
-<div class="sourceCode" id="cb60"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 695.4440 220.0685 695.4440
@@ -636,12 +644,12 @@
## sigma 3.965 NA NA NA
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 100.521 2.74e-10 92.2366 108.805
-## k1 0.124 5.75e-06 0.0958 0.161
-## k2 0.124 6.72e-02 0.0319 0.484
-## g 0.877 5.00e-01 0.0000 1.000
-## sigma 7.048 2.50e-04 4.0349 10.061
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 100.521 2.74e-10 NA NA
+## k1 0.124 2.53e-05 NA NA
+## k2 0.124 2.52e-02 NA NA
+## g 0.793 5.00e-01 NA NA
+## sigma 7.048 2.50e-04 NA NA
##
##
## DTx values:
@@ -656,23 +664,21 @@
<div id="example-on-page-12-lower-panel" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2>
-<div class="sourceCode" id="cb62"><pre class="downlit">
-<span class="va">p12b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p12b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
<pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre>
<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
-<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb72"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
-<div class="sourceCode" id="cb73"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 58.90242 19.06353 58.90242
@@ -696,11 +702,11 @@
##
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 97.6840 NaN NaN NaN
-## k1 0.0589 NaN NA NA
-## k2 0.0589 NaN NA NA
-## g 0.6902 NaN NA NA
-## sigma 3.4323 NaN NaN NaN
+## parent_0 97.6840 NA NaN NaN
+## k1 0.0589 NA NA NA
+## k2 0.0589 NA NA NA
+## g 0.6473 NA NA NA
+## sigma 3.4323 NA NaN NaN
##
##
## DTx values:
@@ -715,15 +721,19 @@
<div id="example-on-page-13" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2>
-<div class="sourceCode" id="cb75"><pre class="downlit">
-<span class="va">p13</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p13</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb78"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
-<div class="sourceCode" id="cb79"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb84"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 174.5971 142.3951 174.5971
@@ -746,12 +756,12 @@
## sigma 3.0811 9.64e-05 1.84296 4.319
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01
-## k1 0.00258 4.28e-01 1.45e-08 4.61e+02
-## k2 0.00258 3.69e-08 2.20e-03 3.03e-03
-## g 0.00442 5.00e-01 0.00e+00 1.00e+00
-## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 92.73500 NA 8.95e+01 95.92118
+## k1 0.00258 NA 4.25e-04 0.01569
+## k2 0.00258 NA 1.76e-03 0.00379
+## g 0.16452 NA NA NA
+## sigma 3.41172 NA 2.02e+00 4.79960
##
##
## DTx values:
@@ -767,19 +777,19 @@
<div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1">
<h1 class="hasAnchor">
<a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1>
-<div class="sourceCode" id="cb81"><pre class="downlit">
-<span class="va">p14</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p14</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb87"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
-<div class="sourceCode" id="cb88"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb93"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 48.43249 28.67746 27.26248
@@ -805,7 +815,7 @@
## 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 7.70e-12 5.00e-01 0.00000 Inf
+## k2 5.33e-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
##
@@ -814,7 +824,7 @@
## 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 2.41e+10 2.33e+11 9.00e+10
+## DFOP 3.48e+10 3.37e+11 1.30e+11
##
## Representative half-life:
## [1] 6697.44</code></pre>
@@ -823,19 +833,15 @@
<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="cb90"><pre class="downlit">
-<span class="va">p15a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful</code></pre>
+<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p15a</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb96"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
-<div class="sourceCode" id="cb97"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 245.5248 135.0132 245.5248
@@ -859,10 +865,10 @@
##
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 97.96752 NA 94.21914 101.7159
-## k1 0.00952 NA 0.00241 0.0377
-## k2 0.00952 NA 0.00747 0.0121
-## g 0.17247 NA NA NA
+## parent_0 97.96751 NA 94.21913 101.7159
+## k1 0.00952 NA 0.00221 0.0411
+## k2 0.00952 NA 0.00626 0.0145
+## g 0.21241 NA 0.00000 1.0000
## sigma 4.18778 NA 2.39747 5.9781
##
##
@@ -874,19 +880,19 @@
##
## Representative half-life:
## [1] 41.33</code></pre>
-<div class="sourceCode" id="cb99"><pre class="downlit">
-<span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb105"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
-<div class="sourceCode" id="cb106"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb108"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 106.91629 68.55574 106.91629
@@ -910,11 +916,11 @@
##
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
-## 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 1.58208 3.94e+00
+## parent_0 1.01e+02 NA 9.82e+01 1.04e+02
+## k1 4.86e-03 NA 8.63e-04 2.73e-02
+## k2 4.86e-03 NA 3.21e-03 7.35e-03
+## g 1.88e-01 NA NA NA
+## sigma 2.76e+00 NA 1.58e+00 3.94e+00
##
##
## DTx values:
@@ -930,17 +936,17 @@
<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="cb108"><pre class="downlit">
-<span class="va">p16</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="va">p16</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre>
<pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre>
<pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre>
-<div class="sourceCode" id="cb113"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb115"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
-<div class="sourceCode" id="cb114"><pre class="downlit">
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></pre></div>
+<div class="sourceCode" id="cb116"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
## 3831.804 2062.008 1550.980
@@ -965,7 +971,7 @@
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
## parent_0 88.5333 7.40e-18 79.9836 97.083
-## k1 18.5560 5.00e-01 0.0000 Inf
+## k1 18.8461 5.00e-01 0.0000 Inf
## k2 0.0776 1.41e-05 0.0518 0.116
## g 0.4733 1.41e-09 0.3674 0.582
## sigma 7.1902 2.11e-08 5.2785 9.102

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