Merge branch 'main' into custom_lsoda_call

author: Johannes Ranke <jranke@uni-bremen.de> 2023-02-13 05:19:08 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2023-02-13 05:19:08 +0100
commit: 8d1a84ac2190538ed3bac53a303064e281595868 (patch)
tree: acb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/articles/web_only/NAFTA_examples.html
parent: 51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent: 4200e566ad2600f56bc3987669aeab88582139eb (diff)
1 files changed, 813 insertions, 798 deletions
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index b9784415..a054d4a1 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -20,6 +20,8 @@
 <![endif]-->
 </head>
 <body data-spy="scroll" data-target="#toc">
+    
+
     <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -32,7 +34,7 @@
       </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">1.0.3.9000</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span>
       </span>
     </div>
 
@@ -42,7 +44,7 @@
   <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>
@@ -58,19 +60,28 @@
       <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
-      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+      <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a>
     </li>
     <li>
       <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
+      <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
     </li>
     <li>
       <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
     <li>
-      <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a>
+      <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
+    </li>
+    <li>
+      <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
     </li>
   </ul>
 </li>
@@ -80,7 +91,7 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="https://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/" class="external-link">
     <span class="fab fa-github fa-lg"></span>
      
   </a>
@@ -95,908 +106,908 @@
 
       
 
-      </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">
+      </header><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 data-toc-skip class="author">Johannes Ranke</h4>
             
-            <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4>
+            <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-24)</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>
+      <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>
 
     </div>
 
     
     
-<div id="introduction" class="section level1">
-<h1 class="hasAnchor">
-<a href="#introduction" class="anchor"></a>Introduction</h1>
+<div class="section level2">
+<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
+</h2>
 <p>In this document, the example evaluations provided in Attachment 1 to the SOP of US EPA for using the NAFTA guidance <span class="citation">(US EPA 2015)</span> are repeated using mkin. The original evaluations reported in the attachment were performed using PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version distributed at the US EPA website today (2019-02-26).</p>
 <p>The datasets are now distributed with the mkin package.</p>
 </div>
-<div id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="anchor"></a>Examples where DFOP did not converge with PestDF 0.8.4</h1>
+<div class="section level2">
+<h2 id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4<a class="anchor" aria-label="anchor" href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4"></a>
+</h2>
 <p>In attachment 1, it is reported that the DFOP model does not converge for these datasets when PestDF 0.8.4 was used. For all four datasets, the DFOP model can be fitted with mkin (see below). The negative half-life given by PestDF 0.8.4 for these fits appears to be the result of a bug. The results for the other two models (SFO and IORE) are the same.</p>
-<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="section level3">
+<h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb4"><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">p5a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 64.4304
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  95.8401 4.67e-21 92.245 99.4357
-## k_parent   0.0102 3.92e-12  0.009  0.0117
-## sigma      4.8230 3.81e-06  3.214  6.4318
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       1.01e+02     NA 9.91e+01 1.02e+02
-## k__iore_parent 1.54e-05     NA 4.08e-06 5.84e-05
-## N_parent       2.57e+00     NA 2.25e+00 2.89e+00
-## sigma          1.68e+00     NA 1.12e+00 2.24e+00
-## 
-## $DFOP
-##          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       2.26e-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
-## 
-## 
-## DTx values:
-##      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 5.59e+11 3.07e+11
-## 
-## Representative half-life:
-## [1] 321.51</code></pre>
+<code class="sourceCode R"><span><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">p5a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 465.21753  56.27506  32.06401 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 64.4304</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  95.8401 4.67e-21 92.245 99.4357</span></span>
+<span><span class="co">## k_parent   0.0102 3.92e-12  0.009  0.0117</span></span>
+<span><span class="co">## sigma      4.8230 3.81e-06  3.214  6.4318</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       1.01e+02     NA 9.91e+01 1.02e+02</span></span>
+<span><span class="co">## k__iore_parent 1.54e-05     NA 4.08e-06 5.84e-05</span></span>
+<span><span class="co">## N_parent       2.57e+00     NA 2.25e+00 2.89e+00</span></span>
+<span><span class="co">## sigma          1.68e+00     NA 1.12e+00 2.24e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span>
+<span><span class="co">## k1       2.67e-02 5.05e-06  0.0243   0.0295</span></span>
+<span><span class="co">## k2       2.26e-12 5.00e-01  0.0000      Inf</span></span>
+<span><span class="co">## g        6.47e-01 3.67e-06  0.6248   0.6677</span></span>
+<span><span class="co">## sigma    1.27e+00 8.91e-06  0.8395   1.6929</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  67.7 2.25e+02 6.77e+01</span></span>
+<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span>
+<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 321.51</span></span></code></pre>
 </div>
-<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="section level3">
+<h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb10"><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">p5b</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 11.77879
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0   96.497 2.32e-24 94.85271 98.14155
-## k_parent    0.008 3.42e-14  0.00737  0.00869
-## sigma       2.295 1.22e-05  1.47976  3.11036
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.85e+01 1.17e-28 9.79e+01 9.92e+01
-## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04
-## N_parent       1.94e+00 5.88e-13 1.76e+00 2.12e+00
-## sigma          7.49e-01 1.63e-05 4.82e-01 1.02e+00
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##      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 1.32e+11 8.04e+10
-## 
-## Representative half-life:
-## [1] 215.87</code></pre>
+<code class="sourceCode R"><span><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">p5b</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 94.81123 10.10936  7.55871 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 11.77879</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0   96.497 2.32e-24 94.85271 98.14155</span></span>
+<span><span class="co">## k_parent    0.008 3.42e-14  0.00737  0.00869</span></span>
+<span><span class="co">## sigma       2.295 1.22e-05  1.47976  3.11036</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span>
+<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span>
+<span><span class="co">## N_parent       1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span>
+<span><span class="co">## sigma          7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span>
+<span><span class="co">## k1       1.55e-02 4.10e-04  0.0143  0.0167</span></span>
+<span><span class="co">## k2       8.63e-12 5.00e-01  0.0000     Inf</span></span>
+<span><span class="co">## g        6.89e-01 2.92e-03  0.6626  0.7142</span></span>
+<span><span class="co">## sigma    6.48e-01 2.38e-05  0.4147  0.8813</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  86.6 2.88e+02 8.66e+01</span></span>
+<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span>
+<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 215.87</span></span></code></pre>
 </div>
-<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="section level3">
+<h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb16"><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">p6</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 58.39888
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower   Upper
-## parent_0  94.7759 7.29e-24 92.3478 97.2039
-## k_parent   0.0179 8.02e-16  0.0166  0.0194
-## sigma      3.0696 3.81e-06  2.0456  4.0936
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       97.12446 2.63e-26 95.62461 98.62431
-## k__iore_parent  0.00252 1.95e-03  0.00134  0.00472
-## N_parent        1.49587 4.07e-13  1.33896  1.65279
-## sigma           1.59698 5.05e-06  1.06169  2.13227
-## 
-## $DFOP
-##          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       3.22e-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
-## 
-## 
-## DTx values:
-##      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 1.01e+10 2.15e+10
-## 
-## Representative half-life:
-## [1] 53.17</code></pre>
+<code class="sourceCode R"><span><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">p6</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 188.45361  51.00699  42.46931 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 58.39888</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7759 7.29e-24 92.3478 97.2039</span></span>
+<span><span class="co">## k_parent   0.0179 8.02e-16  0.0166  0.0194</span></span>
+<span><span class="co">## sigma      3.0696 3.81e-06  2.0456  4.0936</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       97.12446 2.63e-26 95.62461 98.62431</span></span>
+<span><span class="co">## k__iore_parent  0.00252 1.95e-03  0.00134  0.00472</span></span>
+<span><span class="co">## N_parent        1.49587 4.07e-13  1.33896  1.65279</span></span>
+<span><span class="co">## sigma           1.59698 5.05e-06  1.06169  2.13227</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span>
+<span><span class="co">## k1       2.55e-02 7.33e-06  0.0233  0.0278</span></span>
+<span><span class="co">## k2       3.22e-11 5.00e-01  0.0000     Inf</span></span>
+<span><span class="co">## g        8.61e-01 7.55e-06  0.8314  0.8867</span></span>
+<span><span class="co">## sigma    1.46e+00 6.93e-06  0.9661  1.9483</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  38.6 1.28e+02 3.86e+01</span></span>
+<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span>
+<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 53.17</span></span></code></pre>
 </div>
-<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="section level3">
+<h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb22"><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">p7</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 3334.194
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 96.41796 4.80e-53 93.32245 99.51347
-## k_parent  0.00735 7.64e-21  0.00641  0.00843
-## sigma     7.94557 1.83e-15  6.46713  9.42401
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       9.92e+01     NA 9.55e+01 1.03e+02
-## k__iore_parent 1.60e-05     NA 1.45e-07 1.77e-03
-## N_parent       2.45e+00     NA 1.35e+00 3.54e+00
-## sigma          7.42e+00     NA 6.04e+00 8.80e+00
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##      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 3.77e+09 1.91e+09
-## 
-## Representative half-life:
-## [1] 454.55</code></pre>
+<code class="sourceCode R"><span><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">p7</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 3661.661 3195.030 3174.145 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 3334.194</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span>
+<span><span class="co">## k_parent  0.00735 7.64e-21  0.00641  0.00843</span></span>
+<span><span class="co">## sigma     7.94557 1.83e-15  6.46713  9.42401</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.92e+01     NA 9.55e+01 1.03e+02</span></span>
+<span><span class="co">## k__iore_parent 1.60e-05     NA 1.45e-07 1.77e-03</span></span>
+<span><span class="co">## N_parent       2.45e+00     NA 1.35e+00 3.54e+00</span></span>
+<span><span class="co">## sigma          7.42e+00     NA 6.04e+00 8.80e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span>
+<span><span class="co">## k1       1.81e-02 1.75e-01  0.0116   0.0281</span></span>
+<span><span class="co">## k2       3.63e-10 5.00e-01  0.0000      Inf</span></span>
+<span><span class="co">## g        6.06e-01 2.19e-01  0.4826   0.7178</span></span>
+<span><span class="co">## sigma    7.40e+00 2.97e-15  6.0201   8.7754</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  94.3 3.13e+02 9.43e+01</span></span>
+<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span>
+<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 454.55</span></span></code></pre>
 </div>
 </div>
-<div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="anchor"></a>Examples where the representative half-life deviates from the observed DT50</h1>
-<div id="example-on-page-8" class="section level2">
-<h2 class="hasAnchor">
-<a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2>
+<div class="section level2">
+<h2 id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50<a class="anchor" aria-label="anchor" href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50"></a>
+</h2>
+<div class="section level3">
+<h3 id="example-on-page-8">Example on page 8<a class="anchor" aria-label="anchor" href="#example-on-page-8"></a>
+</h3>
 <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 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>
+<code class="sourceCode R"><span><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" class="external-link">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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb28"><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">p8</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 477.4924
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 88.16549 6.53e-29 83.37344 92.95754
-## k_parent  0.00803 1.67e-13  0.00674  0.00957
-## sigma     7.44786 4.17e-10  5.66209  9.23363
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.77e+01 7.03e-35 9.44e+01 1.01e+02
-## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04
-## N_parent       2.27e+00 4.23e-18 2.00e+00 2.54e+00
-## sigma          3.52e+00 5.36e-10 2.67e+00 4.36e+00
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 95.70619 8.99e-32 91.87941 99.53298
-## k1        0.02500 5.25e-04  0.01422  0.04394
-## k2        0.00273 6.84e-03  0.00125  0.00597
-## g         0.58835 2.84e-06  0.36595  0.77970
-## sigma     3.90001 6.94e-10  2.96260  4.83741
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  86.3  287     86.3
-## IORE 53.4  668    201.0
-## DFOP 55.6  517    253.0
-## 
-## Representative half-life:
-## [1] 201.03</code></pre>
+<code class="sourceCode R"><span><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">p8</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 1996.9408  444.9237  547.5616 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 477.4924</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span>
+<span><span class="co">## k_parent  0.00803 1.67e-13  0.00674  0.00957</span></span>
+<span><span class="co">## sigma     7.44786 4.17e-10  5.66209  9.23363</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span>
+<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span>
+<span><span class="co">## N_parent       2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span>
+<span><span class="co">## sigma          3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span>
+<span><span class="co">## k1        0.02500 5.25e-04  0.01422  0.04394</span></span>
+<span><span class="co">## k2        0.00273 6.84e-03  0.00125  0.00597</span></span>
+<span><span class="co">## g         0.58835 2.84e-06  0.36595  0.77970</span></span>
+<span><span class="co">## sigma     3.90001 6.94e-10  2.96260  4.83741</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  86.3  287     86.3</span></span>
+<span><span class="co">## IORE 53.4  668    201.0</span></span>
+<span><span class="co">## DFOP 55.6  517    253.0</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 201.03</span></span></code></pre>
 </div>
 </div>
-<div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1">
-<h1 class="hasAnchor">
-<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study" class="anchor"></a>Examples where SFO was not selected for an abiotic study</h1>
-<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="section level2">
+<h2 id="examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study<a class="anchor" aria-label="anchor" href="#examples-where-sfo-was-not-selected-for-an-abiotic-study"></a>
+</h2>
+<div class="section level3">
+<h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a>
+</h3>
 <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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <div class="sourceCode" id="cb34"><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">p9a</span><span class="op">)</span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></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 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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 105.5678
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower   Upper
-## parent_0  88.1933 3.06e-12 79.9447 96.4419
-## k_parent   0.0409 2.07e-07  0.0324  0.0516
-## sigma      7.2429 3.92e-05  4.4768 10.0090
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       9.89e+01 1.12e-16 9.54e+01 1.02e+02
-## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04
-## N_parent       2.91e+00 1.45e-09 2.50e+00 3.32e+00
-## sigma          2.35e+00 5.31e-05 1.45e+00 3.26e+00
-## 
-## $DFOP
-##          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       9.02e-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
-## 
-## 
-## DTx values:
-##      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 7.69e+11
-## 
-## Representative half-life:
-## [1] 101.43</code></pre>
+<code class="sourceCode R"><span><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">p9a</span><span class="op">)</span></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 839.35238  88.57064   9.93363 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 105.5678</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  88.1933 3.06e-12 79.9447 96.4419</span></span>
+<span><span class="co">## k_parent   0.0409 2.07e-07  0.0324  0.0516</span></span>
+<span><span class="co">## sigma      7.2429 3.92e-05  4.4768 10.0090</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span>
+<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span>
+<span><span class="co">## N_parent       2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span>
+<span><span class="co">## sigma          2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower  Upper</span></span>
+<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span>
+<span><span class="co">## k1       1.38e-01 3.52e-05  0.131  0.146</span></span>
+<span><span class="co">## k2       9.02e-13 5.00e-01  0.000    Inf</span></span>
+<span><span class="co">## g        6.52e-01 8.13e-06  0.642  0.661</span></span>
+<span><span class="co">## sigma    7.88e-01 6.13e-02  0.481  1.095</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  16.9 5.63e+01 1.69e+01</span></span>
+<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span>
+<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 101.43</span></span></code></pre>
 <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p>
 </div>
-<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="section level3">
+<h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a>
+</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>## 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 28.54188
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  94.7123 2.15e-19 93.178 96.2464
-## k_parent   0.0389 4.47e-14  0.037  0.0408
-## sigma      1.5957 1.28e-04  0.932  2.2595
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)   Lower  Upper
-## parent_0         93.863 2.32e-18 92.4565 95.269
-## k__iore_parent    0.127 1.85e-02  0.0504  0.321
-## N_parent          0.711 1.88e-05  0.4843  0.937
-## 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 1.08e-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:
-##      DT50 DT90 DT50_rep
-## SFO  17.8 59.2     17.8
-## IORE 18.4 49.2     14.8
-## DFOP 17.8 59.2     17.8
-## 
-## Representative half-life:
-## [1] 14.8</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 35.64867 23.22334 35.64867 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 28.54188</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7123 2.15e-19 93.178 96.2464</span></span>
+<span><span class="co">## k_parent   0.0389 4.47e-14  0.037  0.0408</span></span>
+<span><span class="co">## sigma      1.5957 1.28e-04  0.932  2.2595</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)   Lower  Upper</span></span>
+<span><span class="co">## parent_0         93.863 2.32e-18 92.4565 95.269</span></span>
+<span><span class="co">## k__iore_parent    0.127 1.85e-02  0.0504  0.321</span></span>
+<span><span class="co">## N_parent          0.711 1.88e-05  0.4843  0.937</span></span>
+<span><span class="co">## sigma             1.288 1.76e-04  0.7456  1.830</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  94.7123 1.61e-16 93.1355 96.2891</span></span>
+<span><span class="co">## k1         0.0389 1.08e-04  0.0266  0.0569</span></span>
+<span><span class="co">## k2         0.0389 2.23e-04  0.0255  0.0592</span></span>
+<span><span class="co">## g          0.5256      NaN      NA      NA</span></span>
+<span><span class="co">## sigma      1.5957 2.50e-04  0.9135  2.2779</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  17.8 59.2     17.8</span></span>
+<span><span class="co">## IORE 18.4 49.2     14.8</span></span>
+<span><span class="co">## DFOP 17.8 59.2     17.8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 14.8</span></span></code></pre>
 <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p>
 </div>
-<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="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">
-<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)): 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 413.4841
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)   Lower    Upper
-## parent_0 101.7315 6.42e-11 91.9259 111.5371
-## k_parent   0.0495 1.70e-07  0.0404   0.0607
-## sigma      8.0152 1.28e-04  4.6813  11.3491
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0          96.86 3.32e-12 90.848 102.863
-## k__iore_parent     2.96 7.91e-02  0.687  12.761
-## N_parent           0.00 5.00e-01 -0.372   0.372
-## sigma              4.90 1.77e-04  2.837   6.968
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)   Lower    Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 6.58e-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
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  14.0 46.5    14.00
-## IORE 16.4 29.4     8.86
-## DFOP 14.0 46.5    14.00
-## 
-## Representative half-life:
-## [1] 8.86</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 899.4089 336.4348 899.4089 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 413.4841</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span>
+<span><span class="co">## k_parent   0.0495 1.70e-07  0.0404   0.0607</span></span>
+<span><span class="co">## sigma      8.0152 1.28e-04  4.6813  11.3491</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0          96.86 3.32e-12 90.848 102.863</span></span>
+<span><span class="co">## k__iore_parent     2.96 7.91e-02  0.687  12.761</span></span>
+<span><span class="co">## N_parent           0.00 5.00e-01 -0.372   0.372</span></span>
+<span><span class="co">## sigma              4.90 1.77e-04  2.837   6.968</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span>
+<span><span class="co">## k1         0.0495 6.58e-03  0.0303   0.0809</span></span>
+<span><span class="co">## k2         0.0495 2.60e-03  0.0410   0.0598</span></span>
+<span><span class="co">## g          0.4487 5.00e-01      NA       NA</span></span>
+<span><span class="co">## sigma      8.0152 2.50e-04  4.5886  11.4418</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  14.0 46.5    14.00</span></span>
+<span><span class="co">## IORE 16.4 29.4     8.86</span></span>
+<span><span class="co">## DFOP 14.0 46.5    14.00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 8.86</span></span></code></pre>
 <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p>
 </div>
 </div>
-<div id="the-dt50-was-not-observed-during-the-study" class="section level1">
-<h1 class="hasAnchor">
-<a href="#the-dt50-was-not-observed-during-the-study" class="anchor"></a>The DT50 was not observed during the study</h1>
-<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="section level2">
+<h2 id="the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study<a class="anchor" aria-label="anchor" href="#the-dt50-was-not-observed-during-the-study"></a>
+</h2>
+<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">
-<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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 251.6944
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 96.15820 4.83e-13 90.24934 1.02e+02
-## k_parent  0.00321 4.71e-05  0.00222 4.64e-03
-## sigma     6.43473 1.28e-04  3.75822 9.11e+00
-## 
-## $IORE
-##                Estimate Pr(&gt;t)    Lower    Upper
-## parent_0       1.05e+02     NA 9.90e+01 1.10e+02
-## k__iore_parent 3.11e-17     NA 1.35e-20 7.18e-14
-## N_parent       8.36e+00     NA 6.62e+00 1.01e+01
-## sigma          3.82e+00     NA 2.21e+00 5.44e+00
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##          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 6.98e+11
-## 
-## Representative half-life:
-## [1] 41148170</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 579.6805 204.7932 144.7783 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 251.6944</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span>
+<span><span class="co">## k_parent  0.00321 4.71e-05  0.00222 4.64e-03</span></span>
+<span><span class="co">## sigma     6.43473 1.28e-04  3.75822 9.11e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       1.05e+02     NA 9.90e+01 1.10e+02</span></span>
+<span><span class="co">## k__iore_parent 3.11e-17     NA 1.35e-20 7.18e-14</span></span>
+<span><span class="co">## N_parent       8.36e+00     NA 6.62e+00 1.01e+01</span></span>
+<span><span class="co">## sigma          3.82e+00     NA 2.21e+00 5.44e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.05e+02 9.47e-13  99.9990 109.1224</span></span>
+<span><span class="co">## k1       4.41e-02 5.95e-03   0.0296   0.0658</span></span>
+<span><span class="co">## k2       9.94e-13 5.00e-01   0.0000      Inf</span></span>
+<span><span class="co">## g        3.22e-01 1.45e-03   0.2814   0.3650</span></span>
+<span><span class="co">## sigma    3.22e+00 3.52e-04   1.8410   4.5906</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##          DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  2.16e+02 7.18e+02 2.16e+02</span></span>
+<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span>
+<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 41148170</span></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>
-<div id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="section level1">
-<h1 class="hasAnchor">
-<a href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="anchor"></a>N is less than 1 and the DFOP rate constants are like the SFO rate constant</h1>
+<div class="section level2">
+<h2 id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate constant<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant"></a>
+</h2>
 <p>In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.</p>
-<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="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">
-<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</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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span>
+<span><span class="co">## matrix</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 270.4679
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower   Upper
-## parent_0  100.521 8.75e-12 92.461 108.581
-## k_parent    0.124 3.61e-08  0.104   0.148
-## sigma       7.048 1.28e-04  4.116   9.980
-## 
-## $IORE
-##                Estimate Pr(&gt;t) Lower Upper
-## parent_0         96.823     NA    NA    NA
-## k__iore_parent    2.436     NA    NA    NA
-## N_parent          0.263     NA    NA    NA
-## 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 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:
-##      DT50 DT90 DT50_rep
-## SFO  5.58 18.5     5.58
-## IORE 6.49 13.2     3.99
-## DFOP 5.58 18.5     5.58
-## 
-## Representative half-life:
-## [1] 3.99</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 695.4440 220.0685 695.4440 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 270.4679</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower   Upper</span></span>
+<span><span class="co">## parent_0  100.521 8.75e-12 92.461 108.581</span></span>
+<span><span class="co">## k_parent    0.124 3.61e-08  0.104   0.148</span></span>
+<span><span class="co">## sigma       7.048 1.28e-04  4.116   9.980</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0         96.823     NA    NA    NA</span></span>
+<span><span class="co">## k__iore_parent    2.436     NA    NA    NA</span></span>
+<span><span class="co">## N_parent          0.263     NA    NA    NA</span></span>
+<span><span class="co">## sigma             3.965     NA    NA    NA</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower   Upper</span></span>
+<span><span class="co">## parent_0  100.521 2.74e-10 92.2366 108.805</span></span>
+<span><span class="co">## k1          0.124 2.53e-05  0.0908   0.170</span></span>
+<span><span class="co">## k2          0.124 2.52e-02  0.0456   0.339</span></span>
+<span><span class="co">## g           0.793      NaN      NA      NA</span></span>
+<span><span class="co">## sigma       7.048 2.50e-04  4.0349  10.061</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  5.58 18.5     5.58</span></span>
+<span><span class="co">## IORE 6.49 13.2     3.99</span></span>
+<span><span class="co">## DFOP 5.58 18.5     5.58</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 3.99</span></span></code></pre>
 </div>
-<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="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">
-<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 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>## 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 51.51756
-## 
-## Parameters:
-## $SFO
-##          Estimate  Pr(&gt;t)   Lower    Upper
-## parent_0  97.6840 0.00039 85.9388 109.4292
-## k_parent   0.0589 0.00261  0.0431   0.0805
-## sigma      3.4323 0.04356 -1.2377   8.1023
-## 
-## $IORE
-##                Estimate Pr(&gt;t)     Lower  Upper
-## parent_0         95.523 0.0055 74.539157 116.51
-## k__iore_parent    0.333 0.1433  0.000717 154.57
-## N_parent          0.568 0.0677 -0.989464   2.13
-## sigma             1.953 0.0975 -5.893100   9.80
-## 
-## $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          0.6473    NaN    NA    NA
-## sigma      3.4323    NaN   NaN   NaN
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  11.8 39.1    11.80
-## IORE 12.9 31.4     9.46
-## DFOP 11.8 39.1    11.80
-## 
-## Representative half-life:
-## [1] 9.46</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 58.90242 19.06353 58.90242 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 51.51756</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate  Pr(&gt;t)   Lower    Upper</span></span>
+<span><span class="co">## parent_0  97.6840 0.00039 85.9388 109.4292</span></span>
+<span><span class="co">## k_parent   0.0589 0.00261  0.0431   0.0805</span></span>
+<span><span class="co">## sigma      3.4323 0.04356 -1.2377   8.1023</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t)     Lower  Upper</span></span>
+<span><span class="co">## parent_0         95.523 0.0055 74.539157 116.51</span></span>
+<span><span class="co">## k__iore_parent    0.333 0.1433  0.000717 154.57</span></span>
+<span><span class="co">## N_parent          0.568 0.0677 -0.989464   2.13</span></span>
+<span><span class="co">## sigma             1.953 0.0975 -5.893100   9.80</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0  97.6840    NaN   NaN   NaN</span></span>
+<span><span class="co">## k1         0.0589    NaN    NA    NA</span></span>
+<span><span class="co">## k2         0.0589    NaN    NA    NA</span></span>
+<span><span class="co">## g          0.6473    NaN    NA    NA</span></span>
+<span><span class="co">## sigma      3.4323    NaN   NaN   NaN</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  11.8 39.1    11.80</span></span>
+<span><span class="co">## IORE 12.9 31.4     9.46</span></span>
+<span><span class="co">## DFOP 11.8 39.1    11.80</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 9.46</span></span></code></pre>
 </div>
-<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="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">
-<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>## 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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 172.131
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 92.73500 5.99e-17 89.61936 95.85065
-## k_parent  0.00258 2.42e-09  0.00223  0.00299
-## sigma     3.41172 7.07e-05  2.05455  4.76888
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower  Upper
-## parent_0        91.6016 6.34e-16 88.53086 94.672
-## k__iore_parent   0.0396 2.36e-01  0.00207  0.759
-## N_parent         0.3541 1.46e-01 -0.35153  1.060
-## sigma            3.0811 9.64e-05  1.84296  4.319
-## 
-## $DFOP
-##          Estimate Pr(&gt;t)    Lower    Upper
-## parent_0 92.73500     NA 8.95e+01 95.92118
-## 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
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO   269  892      269
-## IORE  261  560      169
-## DFOP  269  892      269
-## 
-## Representative half-life:
-## [1] 168.51</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 174.5971 142.3951 174.5971 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 172.131</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span>
+<span><span class="co">## k_parent  0.00258 2.42e-09  0.00223  0.00299</span></span>
+<span><span class="co">## sigma     3.41172 7.07e-05  2.05455  4.76888</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower  Upper</span></span>
+<span><span class="co">## parent_0        91.6016 6.34e-16 88.53086 94.672</span></span>
+<span><span class="co">## k__iore_parent   0.0396 2.36e-01  0.00207  0.759</span></span>
+<span><span class="co">## N_parent         0.3541 1.46e-01 -0.35153  1.060</span></span>
+<span><span class="co">## sigma            3.0811 9.64e-05  1.84296  4.319</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 92.73500     NA 8.95e+01 95.92118</span></span>
+<span><span class="co">## k1        0.00258     NA 4.14e-04  0.01611</span></span>
+<span><span class="co">## k2        0.00258     NA 1.74e-03  0.00383</span></span>
+<span><span class="co">## g         0.16452     NA 0.00e+00  1.00000</span></span>
+<span><span class="co">## sigma     3.41172     NA 2.02e+00  4.79960</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO   269  892      269</span></span>
+<span><span class="co">## IORE  261  560      169</span></span>
+<span><span class="co">## DFOP  269  892      269</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 168.51</span></span></code></pre>
 </div>
 </div>
-<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="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">
-<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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 32.83337
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 99.47124 2.06e-30 98.42254 1.01e+02
-## k_parent  0.00279 3.75e-15  0.00256 3.04e-03
-## sigma     1.55616 3.81e-06  1.03704 2.08e+00
-## 
-## $IORE
-##                Estimate Pr(&gt;t) Lower Upper
-## parent_0       1.00e+02     NA   NaN   NaN
-## k__iore_parent 9.44e-08     NA   NaN   NaN
-## N_parent       3.31e+00     NA   NaN   NaN
-## sigma          1.20e+00     NA 0.796   1.6
-## 
-## $DFOP
-##          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       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
-## 
-## 
-## DTx values:
-##          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 3.05e+10 2.95e+11 1.14e+11
-## 
-## Representative half-life:
-## [1] 6697.44</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 48.43249 28.67746 27.26248 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 32.83337</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span>
+<span><span class="co">## k_parent  0.00279 3.75e-15  0.00256 3.04e-03</span></span>
+<span><span class="co">## sigma     1.55616 3.81e-06  1.03704 2.08e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate Pr(&gt;t) Lower Upper</span></span>
+<span><span class="co">## parent_0       1.00e+02     NA   NaN   NaN</span></span>
+<span><span class="co">## k__iore_parent 9.44e-08     NA   NaN   NaN</span></span>
+<span><span class="co">## N_parent       3.31e+00     NA   NaN   NaN</span></span>
+<span><span class="co">## sigma          1.20e+00     NA 0.796   1.6</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span>
+<span><span class="co">## k1       9.53e-03 1.20e-01  0.00638   0.0143</span></span>
+<span><span class="co">## k2       6.08e-12 5.00e-01  0.00000      Inf</span></span>
+<span><span class="co">## g        3.98e-01 2.19e-01  0.30481   0.4998</span></span>
+<span><span class="co">## sigma    1.17e+00 7.68e-06  0.77406   1.5610</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##          DT50     DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  2.48e+02 8.25e+02 2.48e+02</span></span>
+<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span>
+<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 6697.44</span></span></code></pre>
 <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p>
 </div>
-<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="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">
-<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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 165.9335
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower   Upper
-## parent_0 97.96751 2.00e-15 94.32049 101.615
-## k_parent  0.00952 4.93e-09  0.00824   0.011
-## sigma     4.18778 1.28e-04  2.44588   5.930
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)  Lower  Upper
-## parent_0         95.874 2.94e-15 92.937 98.811
-## k__iore_parent    0.629 2.11e-01  0.044  8.982
-## N_parent          0.000 5.00e-01 -0.642  0.642
-## sigma             3.105 1.78e-04  1.795  4.416
-## 
-## $DFOP
-##          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:
-##      DT50 DT90 DT50_rep
-## SFO  72.8  242     72.8
-## IORE 76.3  137     41.3
-## DFOP 72.8  242     72.8
-## 
-## Representative half-life:
-## [1] 41.33</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 245.5248 135.0132 245.5248 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 165.9335</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower   Upper</span></span>
+<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span>
+<span><span class="co">## k_parent  0.00952 4.93e-09  0.00824   0.011</span></span>
+<span><span class="co">## sigma     4.18778 1.28e-04  2.44588   5.930</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)  Lower  Upper</span></span>
+<span><span class="co">## parent_0         95.874 2.94e-15 92.937 98.811</span></span>
+<span><span class="co">## k__iore_parent    0.629 2.11e-01  0.044  8.982</span></span>
+<span><span class="co">## N_parent          0.000 5.00e-01 -0.642  0.642</span></span>
+<span><span class="co">## sigma             3.105 1.78e-04  1.795  4.416</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span>
+<span><span class="co">## k1        0.00952 6.28e-02  0.00250   0.0363</span></span>
+<span><span class="co">## k2        0.00952 1.27e-04  0.00646   0.0140</span></span>
+<span><span class="co">## g         0.21241 5.00e-01  0.00000   1.0000</span></span>
+<span><span class="co">## sigma     4.18778 2.50e-04  2.39747   5.9781</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  72.8  242     72.8</span></span>
+<span><span class="co">## IORE 76.3  137     41.3</span></span>
+<span><span class="co">## DFOP 72.8  242     72.8</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 41.33</span></span></code></pre>
 <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span class="va">p15b</span> <span class="op">&lt;-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre>
-<pre><code>## Warning in cov2cor(ans$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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre>
+<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span>
+<span><span class="co">## doubtful</span></span></code></pre>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 84.25618
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02
-## k_parent 4.86e-03 2.48e-10  0.00435 5.42e-03
-## sigma    2.76e+00 1.28e-04  1.61402 3.91e+00
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower  Upper
-## 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
-## 
-## $DFOP
-##          Estimate Pr(&gt;t)    Lower    Upper
-## 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:
-##      DT50 DT90 DT50_rep
-## SFO   143  474    143.0
-## IORE  131  236     71.2
-## DFOP  143  474    143.0
-## 
-## Representative half-life:
-## [1] 71.18</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##       SFO      IORE      DFOP </span></span>
+<span><span class="co">## 106.91629  68.55574 106.91629 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 84.25618</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span>
+<span><span class="co">## k_parent 4.86e-03 2.48e-10  0.00435 5.42e-03</span></span>
+<span><span class="co">## sigma    2.76e+00 1.28e-04  1.61402 3.91e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower  Upper</span></span>
+<span><span class="co">## parent_0          99.83 1.81e-16 97.51349 102.14</span></span>
+<span><span class="co">## k__iore_parent     0.38 3.22e-01  0.00352  41.05</span></span>
+<span><span class="co">## N_parent           0.00 5.00e-01 -1.07696   1.08</span></span>
+<span><span class="co">## sigma              2.21 2.57e-04  1.23245   3.19</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0 1.01e+02     NA 9.82e+01 1.04e+02</span></span>
+<span><span class="co">## k1       4.86e-03     NA 8.63e-04 2.73e-02</span></span>
+<span><span class="co">## k2       4.86e-03     NA 3.21e-03 7.35e-03</span></span>
+<span><span class="co">## g        1.88e-01     NA       NA       NA</span></span>
+<span><span class="co">## sigma    2.76e+00     NA 1.58e+00 3.94e+00</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO   143  474    143.0</span></span>
+<span><span class="co">## IORE  131  236     71.2</span></span>
+<span><span class="co">## DFOP  143  474    143.0</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 71.18</span></span></code></pre>
 <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p>
 </div>
-<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="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">
-<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>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre>
+<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre>
+<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre>
+<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre>
 <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>
+<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></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">
-<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 
-## 
-## Critical sum of squares for checking the SFO model:
-## [1] 2247.348
-## 
-## Parameters:
-## $SFO
-##          Estimate   Pr(&gt;t)  Lower Upper
-## parent_0   71.953 2.33e-13 60.509 83.40
-## k_parent    0.159 4.86e-05  0.102  0.25
-## sigma      11.302 1.25e-08  8.308 14.30
-## 
-## $IORE
-##                Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0       8.74e+01 2.48e-16 7.72e+01 97.52972
-## k__iore_parent 4.55e-04 2.16e-01 3.48e-05  0.00595
-## N_parent       2.70e+00 1.21e-08 1.99e+00  3.40046
-## sigma          8.29e+00 1.61e-08 6.09e+00 10.49062
-## 
-## $DFOP
-##          Estimate   Pr(&gt;t)   Lower  Upper
-## parent_0  88.5333 7.40e-18 79.9836 97.083
-## 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
-## 
-## 
-## DTx values:
-##      DT50 DT90 DT50_rep
-## SFO  4.35 14.4     4.35
-## IORE 1.48 32.1     9.67
-## DFOP 0.67 21.4     8.93
-## 
-## Representative half-life:
-## [1] 8.93</code></pre>
+<code class="sourceCode R"><span><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></span></code></pre></div>
+<pre><code><span><span class="co">## Sums of squares:</span></span>
+<span><span class="co">##      SFO     IORE     DFOP </span></span>
+<span><span class="co">## 3831.804 2062.008 1550.980 </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span>
+<span><span class="co">## [1] 2247.348</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Parameters:</span></span>
+<span><span class="co">## $SFO</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)  Lower Upper</span></span>
+<span><span class="co">## parent_0   71.953 2.33e-13 60.509 83.40</span></span>
+<span><span class="co">## k_parent    0.159 4.86e-05  0.102  0.25</span></span>
+<span><span class="co">## sigma      11.302 1.25e-08  8.308 14.30</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $IORE</span></span>
+<span><span class="co">##                Estimate   Pr(&gt;t)    Lower    Upper</span></span>
+<span><span class="co">## parent_0       8.74e+01 2.48e-16 7.72e+01 97.52972</span></span>
+<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05  0.00595</span></span>
+<span><span class="co">## N_parent       2.70e+00 1.21e-08 1.99e+00  3.40046</span></span>
+<span><span class="co">## sigma          8.29e+00 1.61e-08 6.09e+00 10.49062</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## $DFOP</span></span>
+<span><span class="co">##          Estimate   Pr(&gt;t)   Lower  Upper</span></span>
+<span><span class="co">## parent_0  88.5333 7.40e-18 79.9836 97.083</span></span>
+<span><span class="co">## k1        18.8461 5.00e-01  0.0000    Inf</span></span>
+<span><span class="co">## k2         0.0776 1.41e-05  0.0518  0.116</span></span>
+<span><span class="co">## g          0.4733 1.41e-09  0.3674  0.582</span></span>
+<span><span class="co">## sigma      7.1902 2.11e-08  5.2785  9.102</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## DTx values:</span></span>
+<span><span class="co">##      DT50 DT90 DT50_rep</span></span>
+<span><span class="co">## SFO  4.35 14.4     4.35</span></span>
+<span><span class="co">## IORE 1.48 32.1     9.67</span></span>
+<span><span class="co">## DFOP 0.67 21.4     8.93</span></span>
+<span><span class="co">## </span></span>
+<span><span class="co">## Representative half-life:</span></span>
+<span><span class="co">## [1] 8.93</span></span></code></pre>
 <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p>
 </div>
-<div id="conclusions" class="section level1">
-<h1 class="hasAnchor">
-<a href="#conclusions" class="anchor"></a>Conclusions</h1>
+<div class="section level2">
+<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a>
+</h2>
 <p>The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.</p>
 <p>Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.</p>
 </div>
-<div id="references" class="section level1 unnumbered">
-<h1 class="hasAnchor">
-<a href="#references" class="anchor"></a>References</h1>
+<div class="section level2">
+<h2 class="unnumbered" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
+</h2>
 <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>
@@ -1016,11 +1027,13 @@
 
 
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+  <p></p>
+<p>Developed by Johannes Ranke.</p>
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-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@@ -1029,5 +1042,7 @@
   
 
 
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author	Johannes Ranke <jranke@uni-bremen.de>	2023-02-13 05:19:08 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2023-02-13 05:19:08 +0100
commit	8d1a84ac2190538ed3bac53a303064e281595868 (patch)
tree	acb894d85ab7ec87c4911c355a5264a77e08e34b /docs/dev/articles/web_only/NAFTA_examples.html
parent	51d63256a7b3020ee11931d61b4db97b9ded02c0 (diff)
parent	4200e566ad2600f56bc3987669aeab88582139eb (diff)