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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 16:34:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-12 16:34:00 +0200 |
| commit | 6211f3ef4995657798686d8d4ab43ed9406e8a08 (patch) | |
| tree | 4be80cf595880876d51c9cb85f07464b99bc8c83 /docs/articles/web_only/NAFTA_examples.html | |
| parent | c7fcc2f8af47e95cf6164c00a4902340624c13dc (diff) | |
Update vignettes and docs
Diffstat (limited to 'docs/articles/web_only/NAFTA_examples.html')
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 281 |
1 files changed, 118 insertions, 163 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index fecbe3b1..411341b8 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -6,19 +6,19 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance • mkin</title> -<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" 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crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet"> <script src="../../pkgdown.js"></script><meta property="og:title" content="Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance"> -<meta property="og:description" content=""> -<meta name="twitter:card" content="summary"> +<meta property="og:description" content="mkin"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> </head> -<body> +<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"> @@ -31,7 +31,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span> </span> </div> @@ -74,7 +74,14 @@ <a href="../../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"></ul> +<ul class="nav navbar-nav navbar-right"> +<li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> </div> <!--/.nav-collapse --> </div> @@ -87,12 +94,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> + <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-11-01</h4> - + <h4 class="date">2020-05-12</h4> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.Rmd"><code>vignettes/web_only/NAFTA_examples.Rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> </div> @@ -112,12 +119,12 @@ <div id="example-on-page-5-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">p5a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5a"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -143,7 +150,7 @@ ## Estimate Pr(>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 2.86e-12 5.00e-01 0.0000 Inf +## k2 2.17e-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 ## @@ -152,7 +159,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 4.42e+11 2.42e+11 +## DFOP 55.5 5.83e+11 3.20e+11 ## ## Representative half-life: ## [1] 321.51</code></pre> @@ -160,12 +167,12 @@ <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">p5b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p5b"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p5b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p5b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -191,7 +198,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.16e-11 5.00e-01 0.0000 Inf +## k2 1.04e-11 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -200,7 +207,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 9.80e+10 5.98e+10 +## DFOP 83.6 1.09e+11 6.67e+10 ## ## Representative half-life: ## [1] 215.87</code></pre> @@ -208,12 +215,12 @@ <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb13"><html><body><pre class="r"><span class="no">p6</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p6"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb16"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p6</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p6</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -239,7 +246,7 @@ ## Estimate Pr(>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 4.90e-11 5.00e-01 0.0000 Inf +## k2 3.88e-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 ## @@ -248,7 +255,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 6.66e+09 1.41e+10 +## DFOP 34.1 8.42e+09 1.79e+10 ## ## Representative half-life: ## [1] 53.17</code></pre> @@ -256,12 +263,12 @@ <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb19"><html><body><pre class="r"><span class="no">p7</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p7"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb22"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p7</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb23"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p7</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -287,7 +294,7 @@ ## Estimate Pr(>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 1.97e-10 5.00e-01 0.0000 Inf +## k2 2.30e-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 ## @@ -296,7 +303,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 6.97e+09 3.52e+09 +## DFOP 96.4 5.95e+09 3.01e+09 ## ## Representative half-life: ## [1] 454.55</code></pre> @@ -309,12 +316,12 @@ <h2 class="hasAnchor"> <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<div class="sourceCode" id="cb25"><html><body><pre class="r"><span class="no">p8</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p8"</span>]], <span class="kw">parms.ini</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="kw">k__iore_parent_sink</span> <span class="kw">=</span> <span class="fl">1e-3</span>))</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb28"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p8</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p8</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -361,12 +368,12 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="no">p9a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9a"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb35"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -392,7 +399,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 6.02e-13 5.00e-01 0.000 Inf +## k2 6.69e-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 ## @@ -401,7 +408,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 2.07e+12 1.15e+12 +## DFOP 10.5 1.86e+12 1.04e+12 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -410,17 +417,12 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<div class="sourceCode" id="cb37"><html><body><pre class="r"><span class="no">p9b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9b"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb40"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb41"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -447,7 +449,7 @@ ## parent_0 94.7123 1.61e-16 93.1355 96.2891 ## k1 0.0389 1.43e-06 0.0312 0.0485 ## k2 0.0389 6.67e-03 0.0186 0.0812 -## g 0.7742 NaN NA NA +## g 0.7742 5.00e-01 0.0000 1.0000 ## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## @@ -464,12 +466,12 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb43"><html><body><pre class="r"><span class="no">p10</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p10"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb46"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p10</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p10</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -492,12 +494,12 @@ ## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 1.41e-09 91.6534 111.8097 -## k1 0.0495 6.42e-04 0.0301 0.0814 -## k2 0.0495 1.66e-02 0.0200 0.1225 -## g 0.6634 5.00e-01 0.0000 1.0000 -## sigma 8.0152 2.50e-04 4.5886 11.4418 +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 1.41e-09 91.6534 111.810 +## k1 0.0495 6.48e-04 0.0303 0.081 +## k2 0.0495 1.67e-02 0.0201 0.122 +## g 0.6634 5.00e-01 0.0000 1.000 +## sigma 8.0152 2.50e-04 4.5886 11.442 ## ## ## DTx values: @@ -517,12 +519,12 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb49"><html><body><pre class="r"><span class="no">p11</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p11"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb52"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p11</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb53"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p11</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -560,7 +562,7 @@ ## DFOP 4.21e+11 2.64e+12 9.56e+11 ## ## Representative half-life: -## [1] 41148169</code></pre> +## [1] 41148171</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> @@ -571,14 +573,14 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no -## covariance matrix</code></pre> +<div class="sourceCode" id="cb55"><html><body><pre class="r"><span class="no">p12a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12a"</span>]])</pre></body></html></div> +<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance +## matrix</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -603,8 +605,8 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 100.521 2.74e-10 92.2366 108.805 -## k1 0.124 5.74e-06 0.0958 0.161 -## k2 0.124 6.61e-02 0.0319 0.484 +## k1 0.124 5.75e-06 0.0958 0.161 +## k2 0.124 6.72e-02 0.0319 0.484 ## g 0.877 5.00e-01 0.0000 1.000 ## sigma 7.048 2.50e-04 4.0349 10.061 ## @@ -621,20 +623,20 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb62"><html><body><pre class="r"><span class="no">p12b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12b"</span>]])</pre></body></html></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb72"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb73"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -677,16 +679,12 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<div class="sourceCode" id="cb75"><html><body><pre class="r"><span class="no">p13</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb78"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p13</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p13</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -711,9 +709,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 -## k1 0.00258 4.28e-01 1.70e-08 3.92e+02 +## k1 0.00258 4.28e-01 1.45e-08 4.61e+02 ## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 -## g 0.00442 5.00e-01 NA NA +## g 0.00442 5.00e-01 0.00e+00 1.00e+00 ## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## @@ -730,16 +728,16 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb81"><html><body><pre class="r"><span class="no">p14</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb87"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p14</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p14</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -765,7 +763,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 7.29e-12 5.00e-01 0.00000 Inf +## k2 7.70e-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 ## @@ -774,7 +772,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 2.54e+10 2.46e+11 9.51e+10 +## DFOP 2.41e+10 2.33e+11 9.00e+10 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -783,17 +781,16 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb90"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb96"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -816,12 +813,12 @@ ## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 2.85e-13 94.21914 101.7159 -## k1 0.00952 6.80e-02 0.00277 0.0327 -## k2 0.00952 3.82e-06 0.00902 0.0100 -## g 0.17247 NaN NA NA -## sigma 4.18778 2.50e-04 2.39747 5.9781 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 NA 94.21914 101.7159 +## k1 0.00952 NA 0.00241 0.0377 +## k2 0.00952 NA 0.00747 0.0121 +## g 0.17247 NA NA NA +## sigma 4.18778 NA 2.39747 5.9781 ## ## ## DTx values: @@ -832,16 +829,16 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb99"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite -## result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb105"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb106"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -858,18 +855,18 @@ ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51349 102.14 +## parent_0 99.83 1.81e-16 97.51348 102.14 ## k__iore_parent_sink 0.38 3.22e-01 0.00352 41.05 -## N_parent 0.00 5.00e-01 -1.07695 1.08 +## N_parent 0.00 5.00e-01 -1.07696 1.08 ## sigma 2.21 2.57e-04 1.23245 3.19 ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 -## k1 4.86e-03 NA 6.75e-04 3.49e-02 -## k2 4.86e-03 NA 3.37e-03 6.99e-03 +## parent_0 1.01e+02 NA 98.24464 1.04e+02 +## k1 4.86e-03 NA 0.00068 3.47e-02 +## k2 4.86e-03 NA 0.00338 6.99e-03 ## g 1.50e-01 NA NA NA -## sigma 2.76e+00 NA 1.58e+00 3.94e+00 +## sigma 2.76e+00 NA 1.58208 3.94e+00 ## ## ## DTx values: @@ -885,14 +882,14 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb116"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb116-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb108"><html><body><pre class="r"><span class="no">p16</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p16"</span>]])</pre></body></html></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb121"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb121-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb113"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p16</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb114"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p16</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -917,7 +914,7 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.5561 5.00e-01 0.0000 Inf +## k1 18.5560 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 @@ -950,53 +947,11 @@ </div> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <div id="tocnav"> - <h2 class="hasAnchor"> -<a href="#tocnav" class="anchor"></a>Contents</h2> - <ul class="nav nav-pills nav-stacked"> -<li><a href="#introduction">Introduction</a></li> - <li> -<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#example-on-page-5-upper-panel">Example on page 5, upper panel</a></li> - <li><a href="#example-on-page-5-lower-panel">Example on page 5, lower panel</a></li> - <li><a href="#example-on-page-6">Example on page 6</a></li> - <li><a href="#example-on-page-7">Example on page 7</a></li> - </ul> -</li> - <li> -<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#example-on-page-8">Example on page 8</a></li> - </ul> -</li> - <li> -<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#example-on-page-9-upper-panel">Example on page 9, upper panel</a></li> - <li><a href="#example-on-page-9-lower-panel">Example on page 9, lower panel</a></li> - <li><a href="#example-on-page-10">Example on page 10</a></li> - </ul> -</li> - <li> -<a href="#the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study</a><ul class="nav nav-pills nav-stacked"> -<li><a href="#example-on-page-11">Example on page 11</a></li> - </ul> -</li> - <li> -<a href="#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><ul class="nav nav-pills nav-stacked"> -<li><a href="#example-on-page-12-upper-panel">Example on page 12, upper panel</a></li> - <li><a href="#example-on-page-12-lower-panel">Example on page 12, lower panel</a></li> - <li><a href="#example-on-page-13">Example on page 13</a></li> - </ul> -</li> - <li><a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF</a></li> - <li><a href="#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></li> - <li><a href="#the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1</a></li> - <li><a href="#conclusions">Conclusions</a></li> - <li><a href="#references">References</a></li> - </ul> + <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> + </nav> </div> - </div> </div> @@ -1007,7 +962,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> |