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authorJohannes Ranke <jranke@uni-bremen.de>2022-05-18 21:26:17 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-05-18 21:26:17 +0200
commit91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 (patch)
tree8e9e34d18f055936172329c1248e6e2ff136bff9 /docs/articles/web_only/NAFTA_examples.html
parentea57db98cef3fb882f7bd9656b44f270e7bded38 (diff)
Remove outdated comment in FOCUS L vignette, update docs
This also adds the first benchmark results obtained on my laptop system
Diffstat (limited to 'docs/articles/web_only/NAFTA_examples.html')
-rw-r--r--docs/articles/web_only/NAFTA_examples.html154
1 files changed, 75 insertions, 79 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 996e5d49..df1e06db 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -43,7 +43,7 @@
<a href="../../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
@@ -105,7 +105,7 @@
<h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 data-toc-skip class="author">Johannes Ranke</h4>
- <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-03-02)</h4>
+ <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small>
<div class="hidden name"><code>NAFTA_examples.rmd</code></div>
@@ -161,7 +161,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span>
<span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span>
-<span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span>
+<span class="co">## k2 2.95e-12 5.00e-01 0.0000 Inf</span>
<span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span>
<span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span>
<span class="co">## </span>
@@ -170,7 +170,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 67.7 2.25e+02 6.77e+01</span>
<span class="co">## IORE 58.2 1.07e+03 3.22e+02</span>
-<span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span>
+<span class="co">## DFOP 55.5 4.28e+11 2.35e+11</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 321.51</span></code></pre>
@@ -212,7 +212,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span>
<span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span>
-<span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span>
+<span class="co">## k2 9.41e-12 5.00e-01 0.0000 Inf</span>
<span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span>
<span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span>
<span class="co">## </span>
@@ -221,7 +221,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 86.6 2.88e+02 8.66e+01</span>
<span class="co">## IORE 85.5 7.17e+02 2.16e+02</span>
-<span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span>
+<span class="co">## DFOP 83.6 1.21e+11 7.36e+10</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 215.87</span></code></pre>
@@ -263,7 +263,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span>
<span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span>
-<span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span>
+<span class="co">## k2 4.40e-11 5.00e-01 0.0000 Inf</span>
<span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span>
<span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span>
<span class="co">## </span>
@@ -272,7 +272,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 38.6 1.28e+02 3.86e+01</span>
<span class="co">## IORE 34.0 1.77e+02 5.32e+01</span>
-<span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span>
+<span class="co">## DFOP 34.1 7.43e+09 1.58e+10</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 53.17</span></code></pre>
@@ -314,7 +314,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span>
<span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span>
-<span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span>
+<span class="co">## k2 2.81e-10 5.00e-01 0.0000 Inf</span>
<span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span>
<span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span>
<span class="co">## </span>
@@ -323,7 +323,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 94.3 3.13e+02 9.43e+01</span>
<span class="co">## IORE 96.7 1.51e+03 4.55e+02</span>
-<span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span>
+<span class="co">## DFOP 96.4 4.87e+09 2.46e+09</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 454.55</span></code></pre>
@@ -434,7 +434,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 16.9 5.63e+01 1.69e+01</span>
<span class="co">## IORE 11.6 3.37e+02 1.01e+02</span>
-<span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span>
+<span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 101.43</span></code></pre>
@@ -445,17 +445,12 @@
</h3>
<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><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span>
-<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
-<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -482,8 +477,8 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span>
<span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span>
-<span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span>
-<span class="co">## g 0.5256 NaN NA NA</span>
+<span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span>
+<span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span>
<span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span>
<span class="co">## </span>
<span class="co">## </span>
@@ -500,7 +495,7 @@
<div class="section level3">
<h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a>
</h3>
-<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb43"><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><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
@@ -508,10 +503,10 @@
<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
-<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -537,8 +532,8 @@
<span class="co">## $DFOP</span>
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span>
-<span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span>
-<span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span>
+<span class="co">## k1 0.0495 6.32e-03 0.0241 0.1018</span>
+<span class="co">## k2 0.0495 2.41e-03 0.0272 0.0901</span>
<span class="co">## g 0.4487 5.00e-01 NA NA</span>
<span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span>
<span class="co">## </span>
@@ -560,14 +555,14 @@
<div class="section level3">
<h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a>
</h3>
-<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb52"><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><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
-<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -594,7 +589,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span>
<span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span>
-<span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span>
+<span class="co">## k2 9.93e-13 5.00e-01 0.0000 Inf</span>
<span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span>
<span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span>
<span class="co">## </span>
@@ -606,7 +601,7 @@
<span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
-<span class="co">## [1] 41148170</span></code></pre>
+<span class="co">## [1] 41148171</span></code></pre>
<p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p>
</div>
</div>
@@ -617,21 +612,19 @@
<div class="section level3">
<h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a>
</h3>
-<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb58"><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><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span>
+<span class="co">## matrix</span>
+
+<span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span>
<span class="co">## matrix</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span>
-<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
-<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -655,12 +648,12 @@
<span class="co">## sigma 3.965 NA NA NA</span>
<span class="co">## </span>
<span class="co">## $DFOP</span>
-<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
-<span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span>
-<span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span>
-<span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span>
-<span class="co">## g 0.793 NaN NA NA</span>
-<span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span>
+<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
+<span class="co">## parent_0 100.521 NA NA NA</span>
+<span class="co">## k1 0.124 NA NA NA</span>
+<span class="co">## k2 0.124 NA NA NA</span>
+<span class="co">## g 0.793 NA NA NA</span>
+<span class="co">## sigma 7.048 NA NA NA</span>
<span class="co">## </span>
<span class="co">## </span>
<span class="co">## DTx values:</span>
@@ -675,18 +668,17 @@
<div class="section level3">
<h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a>
</h3>
-<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb65"><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><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></code></pre>
<pre><code><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre>
<pre><code><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb80"><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/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
-<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -730,14 +722,18 @@
<div class="section level3">
<h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a>
</h3>
-<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb74"><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><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
+<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
+<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span>
+<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb86"><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-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
-<div class="sourceCode" id="cb87"><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" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -763,9 +759,9 @@
<span class="co">## $DFOP</span>
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span>
-<span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span>
-<span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span>
-<span class="co">## g 0.16452 NA 0.00e+00 1.00000</span>
+<span class="co">## k1 0.00258 NA 4.24e-04 0.01573</span>
+<span class="co">## k2 0.00258 NA 1.76e-03 0.00379</span>
+<span class="co">## g 0.16452 NA NA NA</span>
<span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span>
<span class="co">## </span>
<span class="co">## </span>
@@ -782,7 +778,7 @@
<div class="section level2">
<h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a>
</h2>
-<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb83"><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><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
@@ -790,10 +786,10 @@
<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
-<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -820,7 +816,7 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span>
<span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span>
-<span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span>
+<span class="co">## k2 5.03e-12 5.00e-01 0.00000 Inf</span>
<span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span>
<span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span>
<span class="co">## </span>
@@ -829,7 +825,7 @@
<span class="co">## DT50 DT90 DT50_rep</span>
<span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span>
<span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span>
-<span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span>
+<span class="co">## DFOP 3.69e+10 3.57e+11 1.38e+11</span>
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 6697.44</span></code></pre>
@@ -838,14 +834,18 @@
<div class="section level2">
<h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a>
</h2>
-<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb92"><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><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
+<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
+<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span>
+<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
-<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -871,9 +871,9 @@
<span class="co">## $DFOP</span>
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span>
-<span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span>
-<span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span>
-<span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span>
+<span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span>
+<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span>
+<span class="co">## g 0.21241 5.00e-01 NA NA</span>
<span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span>
<span class="co">## </span>
<span class="co">## </span>
@@ -885,18 +885,14 @@
<span class="co">## </span>
<span class="co">## Representative half-life:</span>
<span class="co">## [1] 41.33</span></code></pre>
-<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre>
-<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span>
-<span class="co">## doubtful</span></code></pre>
<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre>
-<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
-<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -916,15 +912,15 @@
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span>
<span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span>
-<span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span>
+<span class="co">## N_parent 0.00 5.00e-01 -1.07695 1.08</span>
<span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span>
<span class="co">## </span>
<span class="co">## $DFOP</span>
<span class="co">## Estimate Pr(&gt;t) Lower Upper</span>
<span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span>
-<span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span>
+<span class="co">## k1 4.86e-03 NA 8.62e-04 2.74e-02</span>
<span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span>
-<span class="co">## g 1.88e-01 NA NA NA</span>
+<span class="co">## g 1.88e-01 NA 0.00e+00 1.00e+00</span>
<span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span>
<span class="co">## </span>
<span class="co">## </span>
@@ -941,16 +937,16 @@
<div class="section level2">
<h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a>
</h2>
-<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb107"><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><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre>
<pre><code><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></code></pre>
<pre><code><span class="co">## to the terminal degradation rate found with the DFOP model.</span></code></pre>
<pre><code><span class="co">## The representative half-life obtained from the DFOP model may be used</span></code></pre>
-<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb112"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div>
<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
-<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div>
<pre><code><span class="co">## Sums of squares:</span>
<span class="co">## SFO IORE DFOP </span>
@@ -1026,7 +1022,7 @@
<div class="pkgdown">
<p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
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