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diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 57b2ed1c..88551103 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -5,86 +5,71 @@ <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> -<meta name="description" content="mkin"> <title>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance • mkin</title> <script src="../../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> -<link href="../../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"> -<script src="../../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" 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kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul> </li> +<li class="nav-item"><a class="nav-link" href="../../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../../news/index.html">News</a></li> </ul> -<form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../../search.json" id="search-input" placeholder="Search for" autocomplete="off"> -</form> - - <ul class="navbar-nav"> -<li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> - <span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> - + </div> </nav><div class="container template-article"> @@ -93,12 +78,13 @@ <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> + + <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-11-16)</h4> +2025-02-13)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="d-none name"><code>NAFTA_examples.rmd</code></div> @@ -133,7 +119,7 @@ same.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -184,7 +170,7 @@ same.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -235,7 +221,7 @@ same.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -286,7 +272,7 @@ same.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -345,7 +331,7 @@ lower value for the rate constant is used here.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -400,7 +386,7 @@ lower value for the rate constant is used here.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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><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> @@ -454,7 +440,7 @@ suggest a simple exponential decline.</p> <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="cb40"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb41"><pre class="downlit sourceCode r"> <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> @@ -512,7 +498,7 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from <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="cb47"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb48"><pre class="downlit sourceCode r"> <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> @@ -572,7 +558,7 @@ difference in IORE model parameters between PestDF and mkin.</p> <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><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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb54"><pre class="downlit sourceCode r"> <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> @@ -638,7 +624,7 @@ overparameterisation.</p> <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="cb61"><pre class="downlit sourceCode r"> -<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> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb62"><pre class="downlit sourceCode r"> <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> @@ -690,15 +676,14 @@ overparameterisation.</p> <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 pt(abs(tval), rdf, lower.tail = FALSE): 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$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</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="cb73"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb74"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> <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> @@ -742,14 +727,14 @@ overparameterisation.</p> <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="cb76"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p13</span> <span class="op"><-</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="cb79"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb78"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb80"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb79"><pre class="downlit sourceCode r"> <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> @@ -794,18 +779,17 @@ overparameterisation.</p> <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="cb82"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</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$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</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="cb88"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb89"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> <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> @@ -852,18 +836,17 @@ same results in mkin and PestDF.</p> <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="cb91"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p15a</span> <span class="op"><-</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">## 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$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</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="cb97"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb94"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> <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> @@ -903,16 +886,16 @@ same results in mkin and PestDF.</p> <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="cb100"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb97"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</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 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">## 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="cb104"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb105"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> <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> @@ -960,16 +943,16 @@ mkin and PestDF.</p> <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="cb107"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p16</span> <span class="op"><-</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="cb112"><pre class="downlit sourceCode r"> -<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> +<div class="sourceCode" id="cb109"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.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="cb113"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> <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> @@ -1010,10 +993,12 @@ mkin and PestDF.</p> <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> +mkin finds a solution with a much lower +<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msup><mi>χ</mi><mn>2</mn></msup><annotation encoding="application/x-tex">\chi^2</annotation></semantics></math> +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 class="section level2"> <h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> @@ -1038,28 +1023,26 @@ Pesticide Degradation.”</span> <a href="https://www.epa.gov/pesticide-science- </div> </div> </div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside> </div> <footer><div class="pkgdown-footer-left"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> </footer> </div> - - + + </body> </html> |