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1 files changed, 316 insertions, 271 deletions
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index c614166d..b8a5215d 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -88,7 +88,7 @@ <h1>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">2019-07-05</h4> + <h4 class="date">2019-07-09</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -111,13 +111,11 @@ <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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</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="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -128,21 +126,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 1.10e-21 92.121 99.5597 -## k_parent_sink 0.0102 1.71e-12 0.009 0.0117 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 2.37e-26 9.89e+01 1.03e+02 -## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05 -## N_parent 2.57e+00 1.14e-11 2.22e+00 2.92e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.99e+01 4.33e-27 NA NA -## k1 2.67e-02 3.17e-05 NA NA -## k2 2.86e-12 5.00e-01 NA NA -## g 6.47e-01 2.13e-05 NA NA +## 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 +## g 6.47e-01 3.67e-06 0.6248 0.6677 +## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## ## ## DTx values: @@ -152,19 +153,17 @@ ## DFOP 55.5 4.42e+11 2.42e+11 ## ## Representative half-life: -## [1] 321.5119</code></pre> +## [1] 321.51</code></pre> </div> <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -175,21 +174,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.497 2.62e-25 94.77653 98.21774 -## k_parent_sink 0.008 1.35e-14 0.00736 0.00871 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.02e-29 9.78e+01 9.93e+01 -## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04 -## N_parent 1.94e+00 8.18e-13 1.74e+00 2.14e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.84e+01 1.90e-28 NA NA -## k1 1.55e-02 2.83e-03 NA NA -## k2 1.16e-11 5.00e-01 NA NA -## g 6.89e-01 1.31e-02 NA NA +## 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 +## g 6.89e-01 2.92e-03 0.6626 0.7142 +## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## ## ## DTx values: @@ -199,19 +201,17 @@ ## DFOP 83.6 9.80e+10 5.98e+10 ## ## Representative half-life: -## [1] 215.8655</code></pre> +## [1] 215.87</code></pre> </div> <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -222,21 +222,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 1.25e-24 92.2558 97.2960 -## k_parent_sink 0.0179 2.35e-16 0.0166 0.0194 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 97.12446 5.62e-27 95.49343 98.75549 -## k__iore_parent_sink 0.00252 3.54e-03 0.00126 0.00502 -## N_parent 1.49587 6.13e-13 1.32380 1.66794 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.66e+01 4.17e-26 NA NA -## k1 2.55e-02 2.12e-05 NA NA -## k2 4.90e-11 5.00e-01 NA NA -## g 8.61e-01 2.10e-05 NA NA +## 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 +## g 8.61e-01 7.55e-06 0.8314 0.8867 +## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## ## ## DTx values: @@ -246,19 +249,17 @@ ## DFOP 34.1 6.66e+09 1.41e+10 ## ## Representative half-life: -## [1] 53.16582</code></pre> +## [1] 53.17</code></pre> </div> <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -269,21 +270,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 1.52e-53 93.29554 99.54038 -## k_parent_sink 0.00735 3.59e-21 0.00641 0.00842 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.92e+01 7.33e-49 9.53e+01 1.03e+02 -## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03 -## N_parent 2.45e+00 6.14e-05 1.26e+00 3.63e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 8.13e-48 NA NA -## k1 1.81e-02 2.20e-01 NA NA -## k2 1.97e-10 5.00e-01 NA NA -## g 6.06e-01 2.60e-01 NA NA +## 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 +## g 6.06e-01 2.19e-01 0.4826 0.7178 +## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## ## ## DTx values: @@ -293,7 +297,7 @@ ## DFOP 96.4 6.97e+09 3.52e+09 ## ## Representative half-life: -## [1] 454.5528</code></pre> +## [1] 454.55</code></pre> </div> </div> <div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1"> @@ -303,17 +307,12 @@ <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="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" 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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system. - -## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -323,24 +322,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.16549 NA NA NA -## k__iore_parent_sink 0.00100 NA NA NA -## k_parent_sink 0.00803 NA NA NA +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.77e+01 1.05e-35 9.44e+01 1.01e+02 -## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04 -## N_parent 2.27e+00 6.00e-19 2.02e+00 2.53e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 95.70619 NA NA NA -## k__iore_parent_sink 0.00100 NA NA NA -## k1 0.02500 NA NA NA -## k2 0.00273 NA NA NA -## g 0.58835 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.70619 8.99e-32 91.87941 99.53298 +## k1 0.02500 5.25e-04 0.01422 0.04394 +## k2 0.00273 6.84e-03 0.00125 0.00597 +## g 0.58835 2.84e-06 0.36595 0.77970 +## sigma 3.90001 6.94e-10 2.96260 4.83741 ## ## ## DTx values: @@ -350,7 +350,7 @@ ## DFOP 55.6 517 253.0 ## ## Representative half-life: -## [1] 201.0316</code></pre> +## [1] 201.03</code></pre> </div> </div> <div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1"> @@ -359,14 +359,12 @@ <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="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -377,21 +375,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 1.12e-12 79.7671 96.6195 -## k_parent_sink 0.0409 9.50e-08 0.0326 0.0513 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 5.16e-17 9.50e+01 1.03e+02 -## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04 -## N_parent 2.91e+00 3.74e-09 2.43e+00 3.39e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.31e-21 NA NA -## k1 1.38e-01 3.63e-09 NA NA -## k2 6.02e-13 5.00e-01 NA NA -## g 6.52e-01 1.50e-10 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 2.54e-20 97.390 99.672 +## k1 1.38e-01 3.52e-05 0.131 0.146 +## k2 6.02e-13 5.00e-01 0.000 Inf +## g 6.52e-01 8.13e-06 0.642 0.661 +## sigma 7.88e-01 6.13e-02 0.481 1.095 ## ## ## DTx values: @@ -401,20 +402,23 @@ ## DFOP 10.5 2.07e+12 1.15e+12 ## ## Representative half-life: -## [1] 101.4264</code></pre> +## [1] 101.43</code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -424,22 +428,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 2.21e-20 93.0673 96.357 -## k_parent_sink 0.0389 1.48e-14 0.0369 0.041 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 93.863 2.91e-19 92.2996 95.426 -## k__iore_parent_sink 0.127 2.73e-02 0.0457 0.354 -## N_parent 0.711 3.13e-05 0.4605 0.961 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA NA NA -## k1 0.0389 NA NA NA -## k2 0.0389 NA NA NA -## g 0.7742 NA NA NA +## 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 +## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: @@ -449,20 +456,18 @@ ## DFOP 17.8 59.2 17.8 ## ## Representative half-life: -## [1] 14.80012</code></pre> +## [1] 14.8</code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -473,21 +478,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 4.95e-11 90.9683 112.4947 -## k_parent_sink 0.0495 3.40e-07 0.0393 0.0624 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 96.86 2.71e-12 89.884 103.826 -## k__iore_parent_sink 2.96 1.31e-01 0.461 19.020 -## N_parent 0.00 5.00e-01 -0.473 0.473 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 NA NA NA -## k1 0.0495 NA NA NA -## k2 0.0495 NA NA NA -## g 0.6634 NA NA NA +## 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 ## ## ## DTx values: @@ -497,7 +505,7 @@ ## DFOP 14.0 46.5 14.00 ## ## Representative half-life: -## [1] 8.862193</code></pre> +## [1] 8.86</code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> @@ -507,14 +515,12 @@ <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="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -525,21 +531,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 1.56e-13 89.91373 1.02e+02 -## k_parent_sink 0.00321 5.27e-05 0.00218 4.71e-03 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA 9.80e+01 1.11e+02 -## k__iore_parent_sink 3.11e-17 NA 6.88e-25 1.41e-09 -## N_parent 8.36e+00 NA 4.40e+00 1.23e+01 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 7.50e-13 NA NA -## k1 4.41e-02 3.34e-02 NA NA -## k2 7.25e-13 5.00e-01 NA NA -## g 3.22e-01 7.87e-03 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 +## k1 4.41e-02 5.95e-03 0.0296 0.0658 +## k2 7.25e-13 5.00e-01 0.0000 Inf +## g 3.22e-01 1.45e-03 0.2814 0.3650 +## sigma 3.22e+00 3.52e-04 1.8410 4.5906 ## ## ## DTx values: @@ -560,14 +569,14 @@ <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="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" 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 estimate covariance matrix; -## singular system.</code></pre> +<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> <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="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -578,21 +587,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 100.521 5.61e-12 91.687 109.355 -## k_parent_sink 0.124 7.24e-08 0.102 0.152 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.823 1.24e-13 91.5691 102.078 -## k__iore_parent_sink 2.436 3.89e-02 0.7854 7.556 -## N_parent 0.263 3.64e-02 -0.0288 0.554 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 NA NA NA -## k1 0.124 NA NA NA -## k2 0.124 NA NA NA -## g 0.877 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 92.2366 108.805 +## k1 0.124 5.74e-06 0.0958 0.161 +## k2 0.124 6.61e-02 0.0319 0.484 +## g 0.877 5.00e-01 0.0000 1.000 +## sigma 7.048 2.50e-04 4.0349 10.061 ## ## ## DTx values: @@ -602,19 +614,25 @@ ## DFOP 5.58 18.5 5.58 ## ## Representative half-life: -## [1] 3.987308</code></pre> +## [1] 3.99</code></pre> </div> <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -624,22 +642,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 5.36e-05 86.3205 109.0475 -## k_parent_sink 0.0589 9.87e-04 0.0432 0.0803 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.523 0.000386 84.0963 106.95 -## k__iore_parent_sink 0.333 0.170886 0.0103 10.80 -## N_parent 0.568 0.054881 -0.3161 1.45 +## 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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NA NA -## k1 0.0589 NA NA NA -## k2 0.0589 NA NA NA -## g 0.6902 NA NA NA +## parent_0 97.6840 NaN NaN NaN +## k1 0.0589 NaN NA NA +## k2 0.0589 NaN NA NA +## g 0.6902 NaN NA NA +## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: @@ -649,19 +670,21 @@ ## DFOP 11.8 39.1 11.80 ## ## Representative half-life: -## [1] 9.461912</code></pre> +## [1] 9.46</code></pre> </div> <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -671,22 +694,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 1.45e-17 89.3891 96.08094 -## k_parent_sink 0.00258 2.63e-09 0.0022 0.00303 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.6016 2.93e-16 88.08711 95.12 -## k__iore_parent_sink 0.0396 2.81e-01 0.00102 1.53 -## N_parent 0.3541 1.97e-01 -0.51943 1.23 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA NA NA -## k1 0.00258 NA NA NA -## k2 0.00258 NA NA NA -## g 0.00442 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 +## k1 0.00258 4.28e-01 1.70e-08 3.92e+02 +## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 +## g 0.00442 5.00e-01 NA NA +## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## ## DTx values: @@ -696,20 +722,22 @@ ## DFOP 269 892 269 ## ## Representative half-life: -## [1] 168.5123</code></pre> +## [1] 168.51</code></pre> </div> </div> <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -720,21 +748,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 1.71e-31 98.37313 1.01e+02 -## k_parent_sink 0.00279 2.22e-15 0.00255 3.05e-03 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA 9.93e+01 1.01e+02 -## k__iore_parent_sink 9.44e-08 NA 6.81e-11 1.31e-04 -## N_parent 3.31e+00 NA 1.69e+00 4.93e+00 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 2.70e-28 NA NA -## k1 9.53e-03 3.39e-01 NA NA -## k2 7.29e-12 5.00e-01 NA NA -## g 3.98e-01 3.92e-01 NA NA +## 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 +## g 3.98e-01 2.19e-01 0.30481 0.4998 +## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## ## ## DTx values: @@ -744,20 +775,23 @@ ## DFOP 2.54e+10 2.46e+11 9.51e+10 ## ## Representative half-life: -## [1] 6697.437</code></pre> +## [1] 6697.44</code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" 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> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +<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> +<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$cov.unscaled): 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="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -767,22 +801,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 4.98e-16 94.03829 101.8967 -## k_parent_sink 0.00952 5.24e-09 0.00813 0.0112 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.874 8.30e-16 92.5802 99.167 -## k__iore_parent_sink 0.629 2.39e-01 0.0316 12.519 -## N_parent 0.000 5.00e-01 -0.7219 0.722 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 NA NA NA -## k1 0.00952 NA NA NA -## k2 0.00952 NA NA NA -## g 0.17247 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 2.85e-13 94.21914 101.7159 +## k1 0.00952 6.80e-02 0.00277 0.0327 +## k2 0.00952 3.82e-06 0.00902 0.0100 +## g 0.17247 NaN NA NA +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -792,15 +829,17 @@ ## DFOP 72.8 242 72.8 ## ## Representative half-life: -## [1] 41.32749</code></pre> -<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; -## singular system.</code></pre> +## [1] 41.33</code></pre> +<div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<pre><code>## Warning in cov2cor(ans$cov.unscaled): 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="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -811,21 +850,24 @@ ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 4.99e-18 98.12761 1.04e+02 -## k_parent_sink 4.86e-03 1.76e-10 0.00432 5.46e-03 +## 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 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.83 4.49e-17 97.19753 102.5 -## k__iore_parent_sink 0.38 3.41e-01 0.00206 70.0 -## N_parent 0.00 5.00e-01 -1.20105 1.2 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA NA NA -## k1 4.86e-03 NA NA NA -## k2 4.86e-03 NA NA NA -## g 1.50e-01 NA NA NA +## 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 +## g 1.50e-01 NA NA NA +## sigma 2.76e+00 NA 1.58e+00 3.94e+00 ## ## ## DTx values: @@ -835,20 +877,20 @@ ## DFOP 143 474 143.0 ## ## Representative half-life: -## [1] 71.18014</code></pre> +## [1] 71.18</code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" 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="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> <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="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<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://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<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://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -858,22 +900,25 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 3.92e-14 61.087 82.819 -## k_parent_sink 0.159 2.27e-06 0.111 0.229 +## 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 ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 8.74e+01 1.74e-16 7.71e+01 97.70701 -## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05 0.00688 -## N_parent 2.70e+00 1.87e-08 1.97e+00 3.42611 +## 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 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.5333 NA 79.3673 97.699 -## k1 18.5561 NA 0.0000 Inf -## k2 0.0776 NA 0.0471 0.128 -## g 0.4733 NA 0.3138 0.639 +## 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 +## k2 0.0776 1.41e-05 0.0518 0.116 +## g 0.4733 1.41e-09 0.3674 0.582 +## sigma 7.1902 2.11e-08 5.2785 9.102 ## ## ## DTx values: @@ -883,7 +928,7 @@ ## DFOP 0.67 21.4 8.93 ## ## Representative half-life: -## [1] 8.932679</code></pre> +## [1] 8.93</code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> <div id="conclusions" class="section level1"> |