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1 files changed, 90 insertions, 91 deletions
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index fca15672..b9784415 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -32,7 +32,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -81,7 +81,7 @@
<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>
@@ -95,14 +95,13 @@
- </header><link href="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+ </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2020-11-30</h4>
+ <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</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>
@@ -158,7 +157,7 @@
## 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 2.42e-12 5.00e-01 0.0000 Inf
+## k2 2.26e-12 5.00e-01 0.0000 Inf
## g 6.47e-01 3.67e-06 0.6248 0.6677
## sigma 1.27e+00 8.91e-06 0.8395 1.6929
##
@@ -167,7 +166,7 @@
## 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 5.22e+11 2.86e+11
+## DFOP 55.5 5.59e+11 3.07e+11
##
## Representative half-life:
## [1] 321.51</code></pre>
@@ -209,7 +208,7 @@
## 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 1.10e-11 5.00e-01 0.0000 Inf
+## k2 8.63e-12 5.00e-01 0.0000 Inf
## g 6.89e-01 2.92e-03 0.6626 0.7142
## sigma 6.48e-01 2.38e-05 0.4147 0.8813
##
@@ -218,7 +217,7 @@
## 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 1.03e+11 6.29e+10
+## DFOP 83.6 1.32e+11 8.04e+10
##
## Representative half-life:
## [1] 215.87</code></pre>
@@ -260,7 +259,7 @@
## 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 3.60e-11 5.00e-01 0.0000 Inf
+## k2 3.22e-11 5.00e-01 0.0000 Inf
## g 8.61e-01 7.55e-06 0.8314 0.8867
## sigma 1.46e+00 6.93e-06 0.9661 1.9483
##
@@ -269,7 +268,7 @@
## 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 9.07e+09 1.93e+10
+## DFOP 34.1 1.01e+10 2.15e+10
##
## Representative half-life:
## [1] 53.17</code></pre>
@@ -311,7 +310,7 @@
## 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 2.89e-10 5.00e-01 0.0000 Inf
+## k2 3.63e-10 5.00e-01 0.0000 Inf
## g 6.06e-01 2.19e-01 0.4826 0.7178
## sigma 7.40e+00 2.97e-15 6.0201 8.7754
##
@@ -320,7 +319,7 @@
## 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 4.75e+09 2.40e+09
+## DFOP 96.4 3.77e+09 1.91e+09
##
## Representative half-life:
## [1] 454.55</code></pre>
@@ -422,7 +421,7 @@
## 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 9.03e-13 5.00e-01 0.000 Inf
+## k2 9.02e-13 5.00e-01 0.000 Inf
## g 6.52e-01 8.13e-06 0.642 0.661
## sigma 7.88e-01 6.13e-02 0.481 1.095
##
@@ -431,7 +430,7 @@
## 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 1.38e+12 7.67e+11
+## DFOP 10.5 1.38e+12 7.69e+11
##
## Representative half-life:
## [1] 101.43</code></pre>
@@ -443,15 +442,16 @@
<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(diag(covar_notrans)): NaNs produced</code></pre>
<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -475,12 +475,12 @@
## sigma 1.288 1.76e-04 0.7456 1.830
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 94.7123 NA 93.1355 96.2891
-## k1 0.0389 NA 0.0266 0.0569
-## k2 0.0389 NA 0.0255 0.0592
-## g 0.5256 NA NA NA
-## sigma 1.5957 NA 0.9135 2.2779
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 94.7123 1.61e-16 93.1355 96.2891
+## k1 0.0389 1.08e-04 0.0266 0.0569
+## k2 0.0389 2.23e-04 0.0255 0.0592
+## g 0.5256 NaN NA NA
+## sigma 1.5957 2.50e-04 0.9135 2.2779
##
##
## DTx values:
@@ -496,15 +496,18 @@
<div id="example-on-page-10" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2>
-<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">p10</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$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="cb50"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb51"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -530,9 +533,9 @@
## $DFOP
## 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
+## k1 0.0495 6.58e-03 0.0303 0.0809
+## k2 0.0495 2.60e-03 0.0410 0.0598
+## g 0.4487 5.00e-01 NA NA
## sigma 8.0152 2.50e-04 4.5886 11.4418
##
##
@@ -553,14 +556,14 @@
<div id="example-on-page-11" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2>
-<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb56"><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="cb56"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb57"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -596,10 +599,10 @@
## DT50 DT90 DT50_rep
## SFO 2.16e+02 7.18e+02 2.16e+02
## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 3.07e+11 1.93e+12 6.97e+11
+## DFOP 3.07e+11 1.93e+12 6.98e+11
##
## Representative half-life:
-## [1] 41148171</code></pre>
+## [1] 41148170</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>
@@ -610,19 +613,21 @@
<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="downlit sourceCode r">
+<div class="sourceCode" id="cb62"><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>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
+<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
+## doubtful</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb64"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -646,12 +651,12 @@
## sigma 3.965 NA NA NA
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## parent_0 100.521 2.74e-10 NA NA
-## k1 0.124 2.53e-05 NA NA
-## k2 0.124 2.52e-02 NA NA
-## g 0.793 5.00e-01 NA NA
-## sigma 7.048 2.50e-04 NA NA
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 100.521 2.74e-10 92.2366 108.805
+## k1 0.124 2.53e-05 0.0908 0.170
+## k2 0.124 2.52e-02 0.0456 0.339
+## g 0.793 NaN NA NA
+## sigma 7.048 2.50e-04 4.0349 10.061
##
##
## DTx values:
@@ -666,20 +671,18 @@
<div id="example-on-page-12-lower-panel" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2>
-<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">p12b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
<pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre>
<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful</code></pre>
+<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre>
+<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre>
<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
<pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb75"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -704,11 +707,11 @@
##
## $DFOP
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 97.6840 NA NaN NaN
-## k1 0.0589 NA NA NA
-## k2 0.0589 NA NA NA
-## g 0.6473 NA NA NA
-## sigma 3.4323 NA NaN NaN
+## parent_0 97.6840 NaN NaN NaN
+## k1 0.0589 NaN NA NA
+## k2 0.0589 NaN NA NA
+## g 0.6473 NaN NA NA
+## sigma 3.4323 NaN NaN NaN
##
##
## DTx values:
@@ -723,18 +726,14 @@
<div id="example-on-page-13" class="section level2">
<h2 class="hasAnchor">
<a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2>
-<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">p13</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$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="cb83"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb84"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -760,9 +759,9 @@
## $DFOP
## 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
+## k1 0.00258 NA 4.14e-04 0.01611
+## k2 0.00258 NA 1.74e-03 0.00383
+## g 0.16452 NA 0.00e+00 1.00000
## sigma 3.41172 NA 2.02e+00 4.79960
##
##
@@ -779,7 +778,7 @@
<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="cb86"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb89"><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>
@@ -787,10 +786,10 @@
## 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="cb92"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb93"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -817,7 +816,7 @@
## 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 5.33e-12 5.00e-01 0.00000 Inf
+## k2 6.08e-12 5.00e-01 0.00000 Inf
## g 3.98e-01 2.19e-01 0.30481 0.4998
## sigma 1.17e+00 7.68e-06 0.77406 1.5610
##
@@ -826,7 +825,7 @@
## 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 3.48e+10 3.37e+11 1.30e+11
+## DFOP 3.05e+10 2.95e+11 1.14e+11
##
## Representative half-life:
## [1] 6697.44</code></pre>
@@ -835,14 +834,14 @@
<div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1">
<h1 class="hasAnchor">
<a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1>
-<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb98"><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="cb98"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb99"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -866,12 +865,12 @@
## sigma 3.105 1.78e-04 1.795 4.416
##
## $DFOP
-## Estimate Pr(&gt;t) Lower Upper
-## 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
+## Estimate Pr(&gt;t) Lower Upper
+## parent_0 97.96751 2.85e-13 94.21913 101.7159
+## k1 0.00952 6.28e-02 0.00250 0.0363
+## k2 0.00952 1.27e-04 0.00646 0.0140
+## g 0.21241 5.00e-01 0.00000 1.0000
+## sigma 4.18778 2.50e-04 2.39747 5.9781
##
##
## DTx values:
@@ -882,7 +881,7 @@
##
## Representative half-life:
## [1] 41.33</code></pre>
-<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb104"><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>
@@ -890,10 +889,10 @@
## 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="cb107"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb108"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -911,7 +910,7 @@
##
## $IORE
## Estimate Pr(&gt;t) Lower Upper
-## parent_0 99.83 1.81e-16 97.51348 102.14
+## parent_0 99.83 1.81e-16 97.51349 102.14
## k__iore_parent 0.38 3.22e-01 0.00352 41.05
## N_parent 0.00 5.00e-01 -1.07696 1.08
## sigma 2.21 2.57e-04 1.23245 3.19
@@ -938,16 +937,16 @@
<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="cb110"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb113"><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="cb115"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.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="cb116"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div>
<pre><code>## Sums of squares:
## SFO IORE DFOP
@@ -998,7 +997,7 @@
<div id="references" class="section level1 unnumbered">
<h1 class="hasAnchor">
<a href="#references" class="anchor"></a>References</h1>
-<div id="refs" class="references">
+<div id="refs" class="references hanging-indent">
<div id="ref-usepa2015">
<p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p>
</div>

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