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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Example evaluation of FOCUS dataset Z</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 16 January 2018 -(rebuilt 2023-05-19)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> - <div class="hidden name"><code>FOCUS_Z.rmd</code></div> - + <div class="d-none name"><code>FOCUS_Z.rmd</code></div> </div> @@ -302,25 +251,25 @@ accelerate the optimization.</p> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> <pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> -<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span> -<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span> -<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span> -<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span> -<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span> -<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span> -<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre> +<span><span class="co">## Z0_0 96.842440 1.994291 48.5598 4.0226e-42 92.830421 100.854459</span></span> +<span><span class="co">## k_Z0 2.215425 0.118457 18.7023 1.0404e-23 1.989490 2.467019</span></span> +<span><span class="co">## k_Z1 0.478307 0.028257 16.9272 6.2332e-22 0.424709 0.538669</span></span> +<span><span class="co">## k_Z2 0.451642 0.042139 10.7178 1.6304e-14 0.374348 0.544894</span></span> +<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034804 0.098975</span></span> +<span><span class="co">## f_Z2_to_Z3 0.471483 0.058348 8.0806 9.6585e-11 0.357720 0.588287</span></span> +<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.755737</span></span></code></pre> <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## $ff</span></span> <span><span class="co">## Z2_Z3 Z2_sink </span></span> -<span><span class="co">## 0.4715 0.5285 </span></span> +<span><span class="co">## 0.47148 0.52852 </span></span> <span><span class="co">## </span></span> <span><span class="co">## $distimes</span></span> <span><span class="co">## DT50 DT90</span></span> -<span><span class="co">## Z0 0.31288 1.0394</span></span> -<span><span class="co">## Z1 1.44917 4.8141</span></span> -<span><span class="co">## Z2 1.53478 5.0984</span></span> -<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre> +<span><span class="co">## Z0 0.31287 1.0393</span></span> +<span><span class="co">## Z1 1.44917 4.8140</span></span> +<span><span class="co">## Z2 1.53473 5.0983</span></span> +<span><span class="co">## Z3 11.80991 39.2317</span></span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> @@ -334,9 +283,11 @@ not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As -expected, the <span class="math inline">\(\chi^2\)</span> error level is -lower for metabolite Z3 using this model and the graphical fit for Z3 is -improved. However, the covariance matrix is not returned.</p> +expected, the +<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msup><mi>χ</mi><mn>2</mn></msup><annotation encoding="application/x-tex">\chi^2</annotation></semantics></math> +error level is lower for metabolite Z3 using this model and the +graphical fit for Z3 is improved. However, the covariance matrix is not +returned.</p> <div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> <span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> @@ -443,11 +394,11 @@ obtained.</p> <span><span class="co">## </span></span> <span><span class="co">## $SFORB</span></span> <span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span> -<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span> +<span><span class="co">## 2.4471342 0.0075124 0.9519866 0.0800071 0.0000000 0.9347816 </span></span> <span><span class="co">## </span></span> <span><span class="co">## $distimes</span></span> <span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span> -<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span> +<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.267 NA NA</span></span> <span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span> <span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span> <span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre> @@ -470,35 +421,26 @@ Studies on Pesticides in EU Registration</em>. 1.1 ed. <a href="http://esdac.jrc </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js deleted file mode 100644 index ca349fd6..00000000 --- a/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js +++ /dev/null @@ -1,15 +0,0 @@ -// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); 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class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 -to the US EPA SOP for the NAFTA guidance</h1> + + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-05-19)</h4> +2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> - <div class="hidden name"><code>NAFTA_examples.rmd</code></div> - + <div class="d-none name"><code>NAFTA_examples.rmd</code></div> </div> @@ -201,7 +149,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> <span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> -<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.41e-12 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> <span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> <span><span class="co">## </span></span> @@ -210,7 +158,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> <span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> -<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## DFOP 55.5 3.70e+11 2.03e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 321.51</span></span></code></pre> @@ -252,7 +200,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> <span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> -<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 9.07e-12 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> <span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> <span><span class="co">## </span></span> @@ -261,7 +209,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> <span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> -<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## DFOP 83.6 1.25e+11 7.64e+10</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 215.87</span></span></code></pre> @@ -303,7 +251,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> <span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> -<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.84e-11 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> <span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> <span><span class="co">## </span></span> @@ -312,7 +260,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> <span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> -<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## DFOP 34.1 8.50e+09 1.80e+10</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 53.17</span></span></code></pre> @@ -354,7 +302,7 @@ same.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> <span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> -<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 3.62e-10 5.00e-01 0.0000 Inf</span></span> <span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> <span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> <span><span class="co">## </span></span> @@ -363,7 +311,7 @@ same.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> <span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> -<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## DFOP 96.4 3.79e+09 1.92e+09</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 454.55</span></span></code></pre> @@ -477,7 +425,7 @@ lower value for the rate constant is used here.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> <span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> -<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 101.43</span></span></code></pre> @@ -490,17 +438,12 @@ suggest a simple exponential decline.</p> </h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -527,8 +470,8 @@ suggest a simple exponential decline.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> <span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> -<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> -<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span></span> <span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -550,18 +493,15 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from <div class="section level3"> <h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> </h3> -<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb48"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -585,12 +525,12 @@ in PestDF and g in mkin. In mkin, it is restricted to the interval from <span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> <span><span class="co">## </span></span> <span><span class="co">## $DFOP</span></span> -<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> -<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> -<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> -<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> -<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.810</span></span> +<span><span class="co">## k1 0.0495 3.04e-03 0.0188 0.131</span></span> +<span><span class="co">## k2 0.0495 4.92e-04 0.0197 0.124</span></span> +<span><span class="co">## g 0.4487 NaN 0.0000 1.000</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.442</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> <span><span class="co">## DTx values:</span></span> @@ -614,14 +554,14 @@ difference in IORE model parameters between PestDF and mkin.</p> <div class="section level3"> <h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> </h3> -<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -660,7 +600,7 @@ difference in IORE model parameters between PestDF and mkin.</p> <span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> -<span><span class="co">## [1] 41148170</span></span></code></pre> +<span><span class="co">## [1] 41148169</span></span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> @@ -677,21 +617,17 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> </h3> -<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> <pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> <span><span class="co">## matrix</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -719,7 +655,7 @@ overparameterisation.</p> <span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> <span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> <span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> -<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## g 0.793 NaN 0.0000 1.000</span></span> <span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -735,18 +671,20 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> </h3> -<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -790,14 +728,14 @@ overparameterisation.</p> <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb75"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb78"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb79"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -823,8 +761,8 @@ overparameterisation.</p> <span><span class="co">## $DFOP</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> -<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> -<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## k1 0.00258 NA 4.18e-04 0.01592</span></span> +<span><span class="co">## k2 0.00258 NA 1.75e-03 0.00381</span></span> <span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> <span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> <span><span class="co">## </span></span> @@ -842,18 +780,17 @@ overparameterisation.</p> <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -880,7 +817,7 @@ overparameterisation.</p> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> <span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> -<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## k2 5.21e-12 5.00e-01 0.00000 Inf</span></span> <span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> <span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> <span><span class="co">## </span></span> @@ -889,7 +826,7 @@ overparameterisation.</p> <span><span class="co">## DT50 DT90 DT50_rep</span></span> <span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> <span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> -<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## DFOP 3.55e+10 3.44e+11 1.33e+11</span></span> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 6697.44</span></span></code></pre> @@ -900,14 +837,17 @@ same results in mkin and PestDF.</p> <div class="section level2"> <h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> </h2> -<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(V) had non-positive or NA entries; the</span></span> +<span><span class="co">## non-finite result may be dubious</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb94"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -933,9 +873,9 @@ same results in mkin and PestDF.</p> <span><span class="co">## $DFOP</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> <span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> -<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> -<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> -<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span></span> +<span><span class="co">## g 0.21241 5.00e-01 NA NA</span></span> <span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> @@ -947,18 +887,16 @@ same results in mkin and PestDF.</p> <span><span class="co">## </span></span> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 41.33</span></span></code></pre> -<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb97"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> -<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> -<span><span class="co">## is doubtful</span></span></code></pre> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> -<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -976,18 +914,18 @@ same results in mkin and PestDF.</p> <span><span class="co">## </span></span> <span><span class="co">## $IORE</span></span> <span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51348 102.14</span></span> <span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> <span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> <span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> <span><span class="co">## </span></span> <span><span class="co">## $DFOP</span></span> -<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> -<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> -<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> -<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> -<span><span class="co">## g 1.88e-01 NA NA NA</span></span> -<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA NA NA</span></span> +<span><span class="co">## k1 4.86e-03 NA NA NA</span></span> +<span><span class="co">## k2 4.86e-03 NA NA NA</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA NA NA</span></span> <span><span class="co">## </span></span> <span><span class="co">## </span></span> <span><span class="co">## DTx values:</span></span> @@ -1006,16 +944,16 @@ mkin and PestDF.</p> <div class="section level2"> <h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> </h2> -<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> <pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> <pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> <pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> -<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb109"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> <pre><code><span><span class="co">## Sums of squares:</span></span> <span><span class="co">## SFO IORE DFOP </span></span> @@ -1056,10 +994,12 @@ mkin and PestDF.</p> <span><span class="co">## Representative half-life:</span></span> <span><span class="co">## [1] 8.93</span></span></code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as -mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from -the slower rate constant of the DFOP model is larger than the IORE -derived half-life, the NAFTA recommendation obtained with mkin is to use -the DFOP representative half-life of 8.9 days.</p> +mkin finds a solution with a much lower +<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msup><mi>χ</mi><mn>2</mn></msup><annotation encoding="application/x-tex">\chi^2</annotation></semantics></math> +error level. As the half-life from the slower rate constant of the DFOP +model is larger than the IORE derived half-life, the NAFTA +recommendation obtained with mkin is to use the DFOP representative +half-life of 8.9 days.</p> </div> <div class="section level2"> <h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> @@ -1084,35 +1024,26 @@ Pesticide Degradation.”</span> <a href="https://www.epa.gov/pesticide-science- </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js deleted file mode 100644 index ca349fd6..00000000 --- a/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js +++ /dev/null @@ -1,15 +0,0 @@ -// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css deleted file mode 100644 index 07aee5fc..00000000 --- a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css +++ /dev/null @@ -1,4 +0,0 @@ -/* Styles for section anchors */ -a.anchor-section {margin-left: 10px; visibility: hidden; color: inherit;} -a.anchor-section::before {content: '#';} -.hasAnchor:hover a.anchor-section {visibility: visible;} diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js b/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js deleted file mode 100644 index 570f99a0..00000000 --- a/docs/dev/articles/web_only/NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js +++ /dev/null @@ -1,33 +0,0 @@ -// Anchor sections v1.0 written by Atsushi Yasumoto on Oct 3rd, 2020. -document.addEventListener('DOMContentLoaded', function() { - // Do nothing if AnchorJS is used - if (typeof window.anchors === 'object' && anchors.hasOwnProperty('hasAnchorJSLink')) { - return; - } - - const h = document.querySelectorAll('h1, h2, h3, h4, h5, h6'); - - // Do nothing if sections are already anchored - if (Array.from(h).some(x => x.classList.contains('hasAnchor'))) { - return null; - } - - // Use section id when pandoc runs with --section-divs - const section_id = function(x) { - return ((x.classList.contains('section') || (x.tagName === 'SECTION')) - ? 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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Benchmark timings for mkin</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-05-19)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> - <div class="hidden name"><code>benchmarks.rmd</code></div> - + <div class="d-none name"><code>benchmarks.rmd</code></div> </div> @@ -232,7 +181,15 @@ systems. All trademarks belong to their respective owners.</p> </h3> <p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="8%"> +<col width="54%"> +<col width="8%"> +<col width="12%"> +<col width="8%"> +<col width="9%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -436,11 +393,43 @@ models fitted to two datasets, i.e. eight fits for each test.</p> </tr> <tr class="odd"> <td align="left">Linux</td> -<td align="left">Ryzen 9 7950X</td> -<td align="left">4.3.0</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> <td align="left">1.2.5</td> -<td align="right">1.400</td> -<td align="right">1.936</td> +<td align="right">2.369</td> +<td align="right">3.632</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">2.856</td> +<td align="right">4.960</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.2</td> +<td align="left">1.2.6</td> +<td align="right">1.408</td> +<td align="right">2.041</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.9</td> +<td align="right">1.323</td> +<td align="right">1.925</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.10</td> +<td align="right">1.407</td> +<td align="right">1.990</td> </tr> </tbody> </table> @@ -452,6 +441,15 @@ models fitted to two datasets, i.e. eight fits for each test.</p> by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> <table class="table"> +<colgroup> +<col width="7%"> +<col width="50%"> +<col width="7%"> +<col width="11%"> +<col width="7%"> +<col width="8%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -680,12 +678,48 @@ for each test.</p> </tr> <tr class="odd"> <td align="left">Linux</td> -<td align="left">Ryzen 9 7950X</td> -<td align="left">4.3.0</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> <td align="left">1.2.5</td> -<td align="right">0.800</td> -<td align="right">2.118</td> -<td align="right">1.172</td> +<td align="right">1.823</td> +<td align="right">5.555</td> +<td align="right">2.404</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">1.761</td> +<td align="right">5.405</td> +<td align="right">2.462</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.2</td> +<td align="left">1.2.6</td> +<td align="right">0.795</td> +<td align="right">2.228</td> +<td align="right">1.178</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.9</td> +<td align="right">0.754</td> +<td align="right">2.153</td> +<td align="right">1.139</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.10</td> +<td align="right">0.775</td> +<td align="right">2.199</td> +<td align="right">1.161</td> </tr> </tbody> </table> @@ -696,18 +730,18 @@ for each test.</p> <p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> -<table class="table"> +<table style="width:100%;" class="table"> <colgroup> +<col width="5%"> +<col width="40%"> +<col width="5%"> <col width="8%"> -<col width="19%"> -<col width="8%"> -<col width="12%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -<col width="9%"> -<col width="8%"> -<col width="9%"> +<col width="5%"> +<col width="5%"> +<col width="5%"> +<col width="6%"> +<col width="5%"> +<col width="6%"> </colgroup> <thead><tr class="header"> <th align="left">OS</th> @@ -1012,49 +1046,88 @@ dataset, i.e. one fit for each test.</p> </tr> <tr class="odd"> <td align="left">Linux</td> -<td align="left">Ryzen 9 7950X</td> -<td align="left">4.3.0</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> <td align="left">1.2.5</td> +<td align="right">0.798</td> +<td align="right">1.096</td> +<td align="right">1.217</td> +<td align="right">3.173</td> +<td align="right">1.634</td> +<td align="right">2.271</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">0.813</td> +<td align="right">1.136</td> +<td align="right">1.220</td> +<td align="right">3.114</td> +<td align="right">1.598</td> +<td align="right">2.255</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.2</td> +<td align="left">1.2.6</td> +<td align="right">0.439</td> +<td align="right">0.557</td> +<td align="right">0.585</td> +<td align="right">1.338</td> +<td align="right">0.749</td> +<td align="right">0.999</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.9</td> +<td align="right">0.424</td> +<td align="right">0.534</td> +<td align="right">0.560</td> +<td align="right">1.298</td> +<td align="right">0.735</td> +<td align="right">0.981</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.4.2</td> +<td align="left">1.2.10</td> <td align="right">0.433</td> -<td align="right">0.558</td> -<td align="right">0.618</td> -<td align="right">1.053</td> -<td align="right">0.745</td> -<td align="right">0.986</td> +<td align="right">0.541</td> +<td align="right">0.576</td> +<td align="right">1.307</td> +<td align="right">0.744</td> +<td align="right">0.988</td> </tr> </tbody> </table> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a 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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Performance benefit by using compiled model -definitions in mkin</h1> + + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2023-05-19</h4> + <h4 data-toc-skip class="date">2025-02-16</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> - <div class="hidden name"><code>compiled_models.rmd</code></div> - + <div class="d-none name"><code>compiled_models.rmd</code></div> </div> @@ -153,7 +101,7 @@ compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of a compiler using</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <p>In previous versions, it used <code>Sys.which("gcc")</code> for this check.</p> <p>On Linux, you need to have the essential build tools like make and @@ -214,10 +162,10 @@ solution is also implemented, which is included in the tests below.</p> <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.108</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.259 0.136</span></span> -<span><span class="co">## 2 Eigenvalue based 1 1.704 0.184</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 21.574 2.330</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.115</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.217 0.140</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.652 0.190</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 20.522 2.360</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> @@ -248,45 +196,36 @@ compiled code is available.</p> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.178</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 23.708 4.220</span></span></code></pre> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.180</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.656 4.258</span></span></code></pre> <p>Here we get a performance benefit of a factor of 24 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.2.5 on</p> -<pre><code><span><span class="co">## R version 4.3.0 (2023-04-21)</span></span> -<span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> +<p>This vignette was built with mkin 1.2.10 on</p> +<pre><code><span><span class="co">## R version 4.4.2 (2024-10-31)</span></span> +<span><span class="co">## Platform: x86_64-pc-linux-gnu</span></span> <span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre> <pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre> </div> - 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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluations of the dimethenamid data -from 2018</h1> + + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 19 May 2023</h4> +built on 16 Feb 2025</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> - <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> - + <div class="d-none name"><code>dimethenamid_2018.rmd</code></div> </div> @@ -264,7 +212,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK C OK C OK + DFOP OK OK OK OK C OK C: Optimisation did not converge: iteration limit reached without convergence (10) @@ -320,7 +268,7 @@ indicates that this difference is significant as the p-value is below <pre><code> Model df AIC BIC logLik Test L.Ratio p-value f_parent_nlme_sfo_const 1 5 796.60 811.82 -393.30 f_parent_nlme_sfo_tc 2 6 798.60 816.86 -393.30 1 vs 2 0.00 0.998 -f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001</code></pre> +f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 <.0001</code></pre> <p>In addition to these fits, attempts were also made to include correlations between random effects by using the log Cholesky parameterisation of the matrix specifying them. The code used for these @@ -409,11 +357,11 @@ DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 -a.1 1.82141 1.65122 1.9916 -SD.DMTA_0 1.64787 0.45772 2.8380 +a.1 1.82141 1.60516 2.0377 +SD.DMTA_0 1.64787 0.45729 2.8384 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50195 2.5679 -SD.g 1.10266 0.32369 1.8816</code></pre> +SD.k2 0.03296 -2.50524 2.5712 +SD.g 1.10266 0.32354 1.8818</code></pre> <p>While the other parameters converge to credible values, the variance of k2 (<code>omega2.k2</code>) converges to a very small value. The printout of the <code>saem.mmkin</code> model shows that the estimated @@ -447,17 +395,17 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - estimate lower upper -DMTA_0 98.27617 96.3088 100.2436 -k1 0.06437 0.0337 0.0950 -k2 0.00880 0.0063 0.0113 -g 0.95249 0.9100 0.9949 -a.1 1.06161 0.8625 1.2607 -b.1 0.02967 0.0226 0.0367 -SD.DMTA_0 2.06075 0.4187 3.7028 -SD.k1 0.59357 0.2561 0.9310 -SD.k2 0.00292 -10.2960 10.3019 -SD.g 1.05725 0.3808 1.7337</code></pre> + estimate lower upper +DMTA_0 98.24165 96.29190 100.1914 +k1 0.06421 0.03352 0.0949 +k2 0.00866 0.00617 0.0111 +g 0.95340 0.91218 0.9946 +a.1 1.06463 0.87979 1.2495 +b.1 0.02964 0.02266 0.0366 +SD.DMTA_0 2.03611 0.40361 3.6686 +SD.k1 0.59534 0.25692 0.9338 +SD.k2 0.00042 -73.00540 73.0062 +SD.g 1.04234 0.37189 1.7128</code></pre> <p>Doubling the number of iterations in the first phase of the algorithm leads to a slightly lower likelihood, and therefore to slightly higher AIC and BIC values. With even more iterations, the algorithm stops with @@ -489,8 +437,8 @@ comparison function of the saemix package:</p> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.65 663.57 -DFOP tc more iterations 665.88 663.80</code></pre> +DFOP tc 665.67 663.59 +DFOP tc more iterations 665.85 663.76</code></pre> <p>In order to check the influence of the likelihood calculation algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from @@ -505,7 +453,7 @@ the three methods are compared.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -665.65 665.68 665.11 </code></pre> +665.67 665.74 665.13 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value.</p> @@ -530,7 +478,7 @@ using defaults for the fit.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -669.77 669.36 670.95 </code></pre> +670.09 669.37 671.29 </code></pre> </div> </div> <div class="section level3"> @@ -578,15 +526,15 @@ iterations second phase, 15 chains).</p> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">709.26</td> +<td align="right">704.95</td> <td align="right">705.75</td> </tr> <tr class="even"> <td align="left">DFOP</td> <td align="left">tc</td> <td align="right">671.91</td> -<td align="right">665.11</td> -<td align="right">665.65</td> +<td align="right">665.13</td> +<td align="right">665.67</td> </tr> </tbody> </table> @@ -615,13 +563,13 @@ satisfactory precision.</p> </h2> <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.3.0 (2023-04-21) -Platform: x86_64-pc-linux-gnu (64-bit) +<pre><code>R version 4.4.2 (2024-10-31) +Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -638,23 +586,22 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.5 knitr_1.42 +[1] nlme_3.1-166 mkin_1.2.10 knitr_1.49 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 -[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 -[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 -[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 parallel_4.3.0 -[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 -[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 -[37] stringr_1.5.0 fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 -[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 -[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 -[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 -[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> + [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2 + [5] tidyselect_1.2.1 parallel_4.4.2 gridExtra_2.3 jquerylib_0.1.4 + [9] systemfonts_1.1.0 scales_1.3.0 textshaping_0.4.1 yaml_2.3.10 +[13] fastmap_1.2.0 lattice_0.22-6 ggplot2_3.5.1 R6_2.5.1 +[17] generics_0.1.3 lmtest_0.9-40 MASS_7.3-61 htmlwidgets_1.6.4 +[21] tibble_3.2.1 desc_1.4.3 munsell_0.5.1 bslib_0.8.0 +[25] pillar_1.9.0 rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 +[29] xfun_0.49 fs_1.6.5 sass_0.4.9 cli_3.6.3 +[33] pkgdown_2.1.1 magrittr_2.0.3 digest_0.6.37 grid_4.4.2 +[37] npde_3.5 mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 +[41] evaluate_1.0.1 glue_1.8.0 ragg_1.3.3 zoo_1.8-12 +[45] saemix_3.3 fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 +[49] pkgconfig_2.0.3 tools_4.4.2 htmltools_0.5.8.1</code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -679,35 +626,26 @@ November 2017</span>.”</span> <a href="https://open.efsa.europa.eu/study-inven </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> diff --git a/docs/dev/articles/web_only/dimethenamid_2018_files/accessible-code-block-0.0.1/empty-anchor.js 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- </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Short demo of the multistart method</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Short demo of the multistart method</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-05-19)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> - <div class="hidden name"><code>multistart.rmd</code></div> - + <div class="d-none name"><code>multistart.rmd</code></div> </div> @@ -195,43 +144,36 @@ runs:</p> <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> <span><span class="co">## </span></span> <span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> -<span><span class="co">## f_saem_reduced 9 663.73 661.86 -322.86 </span></span> -<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85 0.0361 0 </span></span> -<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89 0.0000 1 1</span></span> -<span><span class="co">## best(f_saem_full_multi) 10 665.56 663.48 -322.78 4.2060 0</span></span></code></pre> +<span><span class="co">## f_saem_reduced 9 663.67 661.80 -322.84 </span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.65 661.78 -322.82 0.0219 0 </span></span> +<span><span class="co">## f_saem_full 10 670.09 668.01 -325.05 0.0000 1 1</span></span> +<span><span class="co">## best(f_saem_full_multi) 10 665.61 663.52 -322.80 4.4870 0</span></span></code></pre> <p>The reduced model results in lower AIC and BIC values, so it is clearly preferable. Using multiple starting values gives a large improvement in case of the full model, because it is less well-defined, which impedes convergence. For the reduced model, using multiple starting values only results in a small improvement of the model fit.</p> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - </div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> diff --git a/docs/dev/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js 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2023-05-19)</h4> +(rebuilt 2025-02-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> - <div class="hidden name"><code>saem_benchmarks.rmd</code></div> - + <div class="d-none name"><code>saem_benchmarks.rmd</code></div> </div> @@ -239,22 +188,22 @@ explanation of the following preprocessing.</p> <tr class="even"> <td align="left">dfop_tc</td> <td align="right">10</td> -<td align="right">669.8</td> -<td align="right">667.7</td> -<td align="right">-324.9</td> +<td align="right">670.1</td> +<td align="right">668.0</td> +<td align="right">-325.0</td> </tr> <tr class="odd"> <td align="left">sforb_tc</td> <td align="right">10</td> -<td align="right">662.8</td> -<td align="right">660.7</td> +<td align="right">662.9</td> +<td align="right">660.8</td> <td align="right">-321.4</td> </tr> <tr class="even"> <td align="left">hs_tc</td> <td align="right">10</td> -<td align="right">667.3</td> -<td align="right">665.2</td> +<td align="right">667.2</td> +<td align="right">665.1</td> <td align="right">-323.6</td> </tr> </tbody> @@ -332,6 +281,16 @@ systems. All trademarks belong to their respective owners.</p> </h3> <p>Constant variance for SFO, DFOP, SFORB and HS.</p> <table class="table"> +<colgroup> +<col width="48%"> +<col width="7%"> +<col width="8%"> +<col width="8%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -414,19 +373,59 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">2.055</td> </tr> <tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">2.998</td> +<td align="right">6.523</td> +<td align="right">6.126</td> +<td align="right">4.721</td> +</tr> +<tr class="odd"> <td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> -<td align="left">1.2.5</td> +<td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">0.994</td> -<td align="right">2.546</td> -<td align="right">1.999</td> -<td align="right">2.070</td> +<td align="right">1.135</td> +<td align="right">2.025</td> +<td align="right">2.406</td> +<td align="right">2.478</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.9</td> +<td align="left">3.3</td> +<td align="right">1.086</td> +<td align="right">1.991</td> +<td align="right">1.949</td> +<td align="right">2.411</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.10</td> +<td align="left">3.3</td> +<td align="right">1.115</td> +<td align="right">2.263</td> +<td align="right">1.991</td> +<td align="right">2.193</td> </tr> </tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> <table class="table"> +<colgroup> +<col width="48%"> +<col width="7%"> +<col width="8%"> +<col width="8%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -509,14 +508,44 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">3.595</td> </tr> <tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">5.070</td> +<td align="right">8.464</td> +<td align="right">8.525</td> +<td align="right">7.599</td> +</tr> +<tr class="odd"> <td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> -<td align="left">1.2.5</td> +<td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">2.152</td> -<td align="right">3.316</td> -<td align="right">3.309</td> -<td align="right">3.337</td> +<td align="right">2.161</td> +<td align="right">3.325</td> +<td align="right">3.669</td> +<td align="right">3.153</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.9</td> +<td align="left">3.3</td> +<td align="right">2.426</td> +<td align="right">3.196</td> +<td align="right">3.256</td> +<td align="right">3.322</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.10</td> +<td align="left">3.3</td> +<td align="right">2.380</td> +<td align="right">3.147</td> +<td align="right">3.131</td> +<td align="right">3.331</td> </tr> </tbody> </table> @@ -525,7 +554,15 @@ systems. All trademarks belong to their respective owners.</p> <h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a> </h3> <p>Two-component error for DFOP-SFO and SFORB-SFO.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="53%"> +<col width="7%"> +<col width="9%"> +<col width="9%"> +<col width="9%"> +<col width="10%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -592,12 +629,36 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">265.934</td> </tr> <tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">30.168</td> +<td align="right">748.675</td> +</tr> +<tr class="odd"> <td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> -<td align="left">1.2.5</td> +<td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">11.249</td> -<td align="right">290.918</td> +<td align="right">12.007</td> +<td align="right">286.757</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.9</td> +<td align="left">3.3</td> +<td align="right">12.420</td> +<td align="right">289.338</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.10</td> +<td align="left">3.3</td> +<td align="right">11.581</td> +<td align="right">296.184</td> </tr> </tbody> </table> @@ -607,6 +668,13 @@ systems. All trademarks belong to their respective owners.</p> </h3> <p>Two-component error for SFORB-SFO3-plus</p> <table class="table"> +<colgroup> +<col width="58%"> +<col width="8%"> +<col width="10%"> +<col width="10%"> +<col width="12%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -665,45 +733,57 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">456.252</td> </tr> <tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">1235.028</td> +</tr> +<tr class="odd"> <td align="left">Ryzen 9 7950X</td> <td align="left">Linux</td> -<td align="left">1.2.5</td> +<td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">479.637</td> +<td align="right">480.577</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.9</td> +<td align="left">3.3</td> +<td align="right">485.836</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.10</td> +<td align="left">3.3</td> +<td align="right">486.856</td> </tr> </tbody> </table> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> - <p></p> -<p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> - <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer> + </footer> </div> - - + </body> </html> diff --git a/docs/dev/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js deleted file mode 100644 index ca349fd6..00000000 --- a/docs/dev/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js +++ /dev/null @@ -1,15 +0,0 @@ -// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> -// v0.0.1 -// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. - -document.addEventListener('DOMContentLoaded', function() { - const codeList = document.getElementsByClassName("sourceCode"); - for (var i = 0; i < codeList.length; i++) { - var linkList = codeList[i].getElementsByTagName('a'); - for (var j = 0; j < linkList.length; j++) { - if (linkList[j].innerHTML === "") { - linkList[j].setAttribute('aria-hidden', 'true'); - } - } - } -}); |
