diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-15 12:53:23 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-15 12:53:23 +0200 |
| commit | 5b1179f0daff9077e1370065f9b9f03a2d0e0450 (patch) | |
| tree | 01f30f5763c279b942458843939d4f02be6ca455 /docs/articles/web_only/NAFTA_examples.html | |
| parent | 272aba066f0d7502e319b7e7f14009318cd44348 (diff) | |
Update online docs for release version
Diffstat (limited to 'docs/articles/web_only/NAFTA_examples.html')
| -rw-r--r-- | docs/articles/web_only/NAFTA_examples.html | 527 |
1 files changed, 284 insertions, 243 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index b91e7ee7..411d4bb8 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -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">0.9.50.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> </span> </div> @@ -68,6 +68,9 @@ <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> + </li> </ul> </li> <li> @@ -76,7 +79,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -97,10 +100,10 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-27</h4> + <h4 class="date">2020-10-15</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> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> + <div class="hidden name"><code>NAFTA_examples.rmd</code></div> </div> @@ -119,12 +122,15 @@ <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"><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> +<div class="sourceCode" id="cb1"><pre class="downlit"> +<span class="va">p5a</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">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb4"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb5"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -134,23 +140,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 4.67e-21 92.245 99.4357 -## k_parent_sink 0.0102 3.92e-12 0.009 0.0117 -## sigma 4.8230 3.81e-06 3.214 6.4318 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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 ## @@ -159,7 +165,7 @@ ## 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> @@ -167,12 +173,15 @@ <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"><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> +<div class="sourceCode" id="cb7"><pre class="downlit"> +<span class="va">p5b</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">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb10"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb11"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -182,23 +191,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497 2.32e-24 94.85271 98.14155 -## k_parent_sink 0.008 3.42e-14 0.00737 0.00869 -## sigma 2.295 1.22e-05 1.47976 3.11036 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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 ## @@ -207,7 +216,7 @@ ## 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> @@ -215,12 +224,15 @@ <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"><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> +<div class="sourceCode" id="cb13"><pre class="downlit"> +<span class="va">p6</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">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb16"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb17"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -230,23 +242,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 7.29e-24 92.3478 97.2039 -## k_parent_sink 0.0179 8.02e-16 0.0166 0.0194 -## sigma 3.0696 3.81e-06 2.0456 4.0936 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 97.12446 2.63e-26 95.62461 98.62431 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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 ## @@ -255,7 +267,7 @@ ## 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> @@ -263,12 +275,15 @@ <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"><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> +<div class="sourceCode" id="cb19"><pre class="downlit"> +<span class="va">p7</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">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb22"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb23"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -278,23 +293,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 4.80e-53 93.32245 99.51347 -## k_parent_sink 0.00735 7.64e-21 0.00641 0.00843 -## sigma 7.94557 1.83e-15 6.46713 9.42401 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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 ## @@ -303,7 +318,7 @@ ## 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> @@ -316,12 +331,15 @@ <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"><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> +<div class="sourceCode" id="cb25"><pre class="downlit"> +<span class="va">p8</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">"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></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb28"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb29"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -331,17 +349,17 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.16549 6.53e-29 83.37344 92.95754 -## k_parent_sink 0.00803 1.67e-13 0.00674 0.00957 -## sigma 7.44786 4.17e-10 5.66209 9.23363 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>t) Lower Upper @@ -368,12 +386,15 @@ <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"><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> +<div class="sourceCode" id="cb31"><pre class="downlit"> +<span class="va">p9a</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">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="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> +<div class="sourceCode" id="cb34"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<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> +<div class="sourceCode" id="cb35"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -383,23 +404,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 3.06e-12 79.9447 96.4419 -## k_parent_sink 0.0409 2.07e-07 0.0324 0.0516 -## sigma 7.2429 3.92e-05 4.4768 10.0090 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 -## k__iore_parent_sink 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 +## Estimate Pr(>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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 6.02e-13 5.00e-01 0.000 Inf +## k2 6.69e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -408,7 +429,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 2.07e+12 1.15e+12 +## DFOP 10.5 1.86e+12 1.04e+12 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -417,17 +438,15 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb37"><html><body><pre class="r"><span class="no">p9b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9b"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> +<div class="sourceCode" id="cb37"><pre class="downlit"> +<span class="va">p9b</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">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb44"><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> +<div class="sourceCode" id="cb40"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><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> +<div class="sourceCode" id="cb41"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -437,24 +456,24 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 2.15e-19 93.178 96.2464 -## k_parent_sink 0.0389 4.47e-14 0.037 0.0408 -## sigma 1.5957 1.28e-04 0.932 2.2595 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 93.863 2.32e-18 92.4565 95.269 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>t) Lower Upper ## 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 ## ## @@ -471,12 +490,15 @@ <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"><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> +<div class="sourceCode" id="cb43"><pre class="downlit"> +<span class="va">p10</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">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb50"><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> +<div class="sourceCode" id="cb46"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb51"><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> +<div class="sourceCode" id="cb47"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -486,25 +508,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 6.42e-11 91.9259 111.5371 -## k_parent_sink 0.0495 1.70e-07 0.0404 0.0607 -## sigma 8.0152 1.28e-04 4.6813 11.3491 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 96.86 3.32e-12 90.848 102.863 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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: @@ -524,12 +546,15 @@ <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"><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> +<div class="sourceCode" id="cb49"><pre class="downlit"> +<span class="va">p11</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">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb56"><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> +<div class="sourceCode" id="cb52"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb57"><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> +<div class="sourceCode" id="cb53"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -539,17 +564,17 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 -## k_parent_sink 0.00321 4.71e-05 0.00222 4.64e-03 -## sigma 6.43473 1.28e-04 3.75822 9.11e+00 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>t) Lower Upper @@ -567,7 +592,7 @@ ## 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> @@ -578,14 +603,17 @@ <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"><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> +<div class="sourceCode" id="cb55"><pre class="downlit"> +<span class="va">p12a</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">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></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"><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> +<div class="sourceCode" id="cb59"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb64"><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> +<div class="sourceCode" id="cb60"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -595,23 +623,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 8.75e-12 92.461 108.581 -## k_parent_sink 0.124 3.61e-08 0.104 0.148 -## sigma 7.048 1.28e-04 4.116 9.980 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 96.823 NA NA NA -## k__iore_parent_sink 2.436 NA NA NA -## N_parent 0.263 NA NA NA -## sigma 3.965 NA NA NA +## Estimate Pr(>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(>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 ## @@ -628,7 +656,8 @@ <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"><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> +<div class="sourceCode" id="cb62"><pre class="downlit"> +<span class="va">p12b</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">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> @@ -639,9 +668,11 @@ ## 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"><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> +<div class="sourceCode" id="cb72"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb77"><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> +<div class="sourceCode" id="cb73"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -651,17 +682,17 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 0.00039 85.9388 109.4292 -## k_parent_sink 0.0589 0.00261 0.0431 0.0805 -## sigma 3.4323 0.04356 -1.2377 8.1023 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 95.523 0.0055 74.539157 116.51 -## k__iore_parent_sink 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 +## Estimate Pr(>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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper @@ -684,16 +715,15 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="no">p13</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> +<div class="sourceCode" id="cb75"><pre class="downlit"> +<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></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb85"><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> +<div class="sourceCode" id="cb78"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb86"><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> +<div class="sourceCode" id="cb79"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -703,24 +733,24 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 5.99e-17 89.61936 95.85065 -## k_parent_sink 0.00258 2.42e-09 0.00223 0.00299 -## sigma 3.41172 7.07e-05 2.05455 4.76888 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 91.6016 6.34e-16 88.53086 94.672 -## k__iore_parent_sink 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 +## Estimate Pr(>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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 -## k1 0.00258 4.28e-01 1.70e-08 3.92e+02 +## k1 0.00258 4.28e-01 1.45e-08 4.61e+02 ## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 -## g 0.00442 5.00e-01 NA NA +## g 0.00442 5.00e-01 0.00e+00 1.00e+00 ## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## @@ -737,16 +767,19 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="no">p14</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb81"><pre class="downlit"> +<span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb94"><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> +<div class="sourceCode" id="cb87"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb95"><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> +<div class="sourceCode" id="cb88"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -756,23 +789,23 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 -## k_parent_sink 0.00279 3.75e-15 0.00256 3.04e-03 -## sigma 1.55616 3.81e-06 1.03704 2.08e+00 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 1.00e+02 NA NaN NaN -## k__iore_parent_sink 9.44e-08 NA NaN NaN -## N_parent 3.31e+00 NA NaN NaN -## sigma 1.20e+00 NA 0.796 1.6 +## Estimate Pr(>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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 7.29e-12 5.00e-01 0.00000 Inf +## k2 7.70e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## @@ -781,7 +814,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 2.54e+10 2.46e+11 9.51e+10 +## DFOP 2.41e+10 2.33e+11 9.00e+10 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -790,17 +823,19 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb90"><pre class="downlit"> +<span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb104"><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> +<div class="sourceCode" id="cb96"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb105"><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> +<div class="sourceCode" id="cb97"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -810,25 +845,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 2.00e-15 94.32049 101.615 -## k_parent_sink 0.00952 4.93e-09 0.00824 0.011 -## sigma 4.18778 1.28e-04 2.44588 5.930 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 95.874 2.94e-15 92.937 98.811 -## k__iore_parent_sink 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 +## Estimate Pr(>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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 2.85e-13 94.21914 101.7159 -## k1 0.00952 6.80e-02 0.00277 0.0327 -## k2 0.00952 3.82e-06 0.00902 0.0100 -## g 0.17247 NaN NA NA -## sigma 4.18778 2.50e-04 2.39747 5.9781 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 NA 94.21914 101.7159 +## k1 0.00952 NA 0.00241 0.0377 +## k2 0.00952 NA 0.00747 0.0121 +## g 0.17247 NA NA NA +## sigma 4.18778 NA 2.39747 5.9781 ## ## ## DTx values: @@ -839,16 +874,19 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb107"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb99"><pre class="downlit"> +<span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb113"><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> +<div class="sourceCode" id="cb105"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<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">p15b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb106"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -858,25 +896,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 -## k_parent_sink 4.86e-03 2.48e-10 0.00435 5.42e-03 -## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51349 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 -## sigma 2.21 2.57e-04 1.23245 3.19 +## Estimate Pr(>t) Lower Upper +## parent_0 99.83 1.81e-16 97.51348 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(>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: @@ -892,14 +930,17 @@ <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"><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> +<div class="sourceCode" id="cb108"><pre class="downlit"> +<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></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb121"><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> +<div class="sourceCode" id="cb113"><pre class="downlit"> +<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb122"><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> +<div class="sourceCode" id="cb114"><pre class="downlit"> +<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></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -909,22 +950,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 2.33e-13 60.509 83.40 -## k_parent_sink 0.159 4.86e-05 0.102 0.25 -## sigma 11.302 1.25e-08 8.308 14.30 +## Estimate Pr(>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(>t) Lower Upper -## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 -## k__iore_parent_sink 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 +## Estimate Pr(>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(>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 @@ -972,7 +1013,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> |