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class="external-link">Wissenschaftlicher Berater, Kronacher +Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke" class="external-link">Privatdozent at the +University of Bremen</a></p> +<div class="section level2"> +<h2 id="the-data">The data<a class="anchor" aria-label="anchor" href="#the-data"></a> +</h2> +<p>The following code defines the example dataset from Appendix 7 to the +FOCUS kinetics report <span class="citation">(FOCUS Work Group on +Degradation Kinetics 2014, 354)</span>.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span></span> +<span><span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,</span> +<span> <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,</span> +<span> Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</span> +<span> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</span> +<span> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</span> +<span> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</span> +<span> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="parent-and-one-metabolite">Parent and one metabolite<a class="anchor" aria-label="anchor" href="#parent-and-one-metabolite"></a> +</h2> +<p>The next step is to set up the models used for the kinetic analysis. +As the simultaneous fit of parent and the first metabolite is usually +straightforward, Step 1 (SFO for parent only) is skipped here. We start +with the model 2a, with formation and decline of metabolite Z1 and the +pathway from parent directly to sink included (default in mkin).</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.2a</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><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="op">)</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> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> +<div class="sourceCode" id="cb7"><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.2a</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 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> +<p>As obvious from the parameter summary (the component of the summary), +the kinetic rate constant from parent compound Z to sink is very small +and the t-test for this parameter suggests that it is not significantly +different from zero. This suggests, in agreement with the analysis in +the FOCUS kinetics report, to simplify the model by removing the pathway +to sink.</p> +<p>A similar result can be obtained when formation fractions are used in +the model formulation:</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.2a.ff</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><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="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</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> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> +<div class="sourceCode" id="cb14"><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.2a.ff</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 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> +<p>Here, the ilr transformed formation fraction fitted in the model +takes a very large value, and the backtransformed formation fraction +from parent Z to Z1 is practically unity. Here, the covariance matrix +used for the calculation of confidence intervals is not returned as the +model is overparameterised.</p> +<p>A simplified model is obtained by removing the pathway to the sink. +</p> +<p>In the following, we use the parameterisation with formation +fractions in order to be able to compare with the results in the FOCUS +guidance, and as it makes it easier to use parameters obtained in a +previous fit when adding a further metabolite.</p> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.3</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="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</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> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> +<div class="sourceCode" id="cb21"><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.3</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 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span> +<span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span> +<span><span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span></span> +<span><span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></span></code></pre> +<p>As there is only one transformation product for Z0 and no pathway to +sink, the formation fraction is internally fixed to unity.</p> +</div> +<div class="section level2"> +<h2 id="metabolites-z2-and-z3">Metabolites Z2 and Z3<a class="anchor" aria-label="anchor" href="#metabolites-z2-and-z3"></a> +</h2> +<p>As suggested in the FOCUS report, the pathway to sink was removed for +metabolite Z1 as well in the next step. While this step appears +questionable on the basis of the above results, it is followed here for +the purpose of comparison. Also, in the FOCUS report, it is assumed that +there is additional empirical evidence that Z1 quickly and exclusively +hydrolyses to Z2.</p> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.5</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> +<span> Z2 <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="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</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> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> +<p>Finally, metabolite Z3 is added to the model. We use the optimised +differential equation parameter values from the previous fit in order to +accelerate the optimization.</p> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.FOCUS</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> +<span> Z2 <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">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <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="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</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> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span></code></pre> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span></code></pre> +<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></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 96.842440 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">## 0.47148 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 0.31287 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> +</div> +<div class="section level2"> +<h2 id="using-the-sforb-model">Using the SFORB model<a class="anchor" aria-label="anchor" href="#using-the-sforb-model"></a> +</h2> +<p>As the FOCUS report states, there is a certain tailing of the time +course of metabolite Z3. Also, the time course of the parent compound is +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 +<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> +<span> Z2 <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">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</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> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations</span></span> +<span><span class="co">## with value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb43"><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.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> +<pre><code><span><span class="co">## NULL</span></span></code></pre> +<p>Therefore, a further stepwise model building is performed starting +from the stage of parent and two metabolites, starting from the +assumption that the model fit for the parent compound can be improved by +using the SFORB model.</p> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.3</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">"SFORB"</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> +<span> Z2 <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="op">)</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> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations</span></span> +<span><span class="co">## with value of zero were removed from the data</span></span></code></pre> +<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> +<p>This results in a much better representation of the behaviour of the +parent compound Z0.</p> +<p>Finally, Z3 is added as well. These models appear overparameterised +(no covariance matrix returned) if the sink for Z1 is left in the +models.</p> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.4</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">"SFORB"</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> +<span> Z2 <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">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <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="op">)</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> +<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span></span> +<span><span class="co">## data</span></span></code></pre> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> +<p>The error level of the fit, but especially of metabolite Z3, can be +improved if the SFORB model is chosen for this metabolite, as this model +is capable of representing the tailing of the metabolite decline +phase.</p> +<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.5</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">"SFORB"</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> +<span> Z2 <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">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</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> +<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span></span> +<span><span class="co">## the data</span></span></code></pre> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> +<p>The summary view of the backtransformed parameters shows that we get +no confidence intervals due to overparameterisation. As the optimized is +excessively small, it seems reasonable to fix it to zero.</p> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,</span> +<span> k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span></span> +<span><span class="co">## from the data</span></span></code></pre> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> +<p>As expected, the residual plots for Z0 and Z3 are more random than in +the case of the all SFO model for which they were shown above. In +conclusion, the model is proposed as the best-fit model for the dataset +from Appendix 7 of the FOCUS report.</p> +<p>A graphical representation of the confidence intervals can finally be +obtained.</p> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> +<p>The endpoints obtained with this model are</p> +<div class="sourceCode" id="cb64"><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.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span></span> +<span><span class="co">## 1.00000 0.53656 0.46344 1.00000 </span></span> +<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">## 2.4471342 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 92.267 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> +<p>It is clear the degradation rate of Z3 towards the end of the +experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the +system of two differential equations representing the SFORB system for +Z3, corresponding to the slower rate constant of the DFOP model) is +reported to be infinity. However, this appears to be a feature of the +data.</p> +</div> +<div class="section level2"> +<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> +<!-- vim: set foldmethod=syntax: --> +<div id="refs" class="references csl-bib-body hanging-indent"> +<div id="ref-FOCUSkinetics2014" class="csl-entry"> +FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for +Estimating Persistence and Degradation Kinetics from Environmental Fate +Studies on Pesticides in EU Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. +</div> +</div> +</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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> +</html> diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differnew file mode 100644 index 00000000..98bc135b --- /dev/null +++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differnew file mode 100644 index 00000000..c1011a35 --- /dev/null +++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png 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href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart 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href="../../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../../news/index.html">News</a></li> + </ul> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul> +</div> + + + </div> +</nav><div class="container template-article"> + + + + +<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 +2025-02-14)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> + <div class="d-none name"><code>NAFTA_examples.rmd</code></div> + </div> + + + +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> +<p>In this document, the example evaluations provided in Attachment 1 to +the SOP of US EPA for using the NAFTA guidance <span class="citation">(US EPA 2015)</span> are repeated using mkin. The +original evaluations reported in the attachment were performed using +PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version +distributed at the US EPA website today (2019-02-26).</p> +<p>The datasets are now distributed with the mkin package.</p> +</div> +<div class="section level2"> +<h2 id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4<a class="anchor" aria-label="anchor" href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4"></a> +</h2> +<p>In attachment 1, it is reported that the DFOP model does not converge +for these datasets when PestDF 0.8.4 was used. For all four datasets, +the DFOP model can be fitted with mkin (see below). The negative +half-life given by PestDF 0.8.4 for these fits appears to be the result +of a bug. The results for the other two models (SFO and IORE) are the +same.</p> +<div class="section level3"> +<h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a> +</h3> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 465.21753 56.27506 32.06401 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 64.4304</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span></span> +<span><span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span></span> +<span><span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span></span> +<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 1.01e+02 NA 9.91e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span></span> +<span><span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span></span> +<span><span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</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 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 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> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 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> +</div> +<div class="section level3"> +<h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a> +</h3> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 94.81123 10.10936 7.55871 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 11.77879</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span></span> +<span><span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span></span> +<span><span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span></span> +<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 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span> +<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span> +<span><span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span> +<span><span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</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 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 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> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 1.25e+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> +</div> +<div class="section level3"> +<h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a> +</h3> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 188.45361 51.00699 42.46931 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 58.39888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span></span> +<span><span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span></span> +<span><span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span></span> +<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 97.12446 2.63e-26 95.62461 98.62431</span></span> +<span><span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span></span> +<span><span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span></span> +<span><span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</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 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 3.84e-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> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 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> +</div> +<div class="section level3"> +<h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a> +</h3> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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="cb22"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3661.661 3195.030 3174.145 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 3334.194</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span> +<span><span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span></span> +<span><span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span></span> +<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 9.92e+01 NA 9.55e+01 1.03e+02</span></span> +<span><span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span></span> +<span><span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span></span> +<span><span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</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 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 3.62e-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> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 3.79e+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> +</div> +</div> +<div class="section level2"> +<h2 id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the +observed DT50<a class="anchor" aria-label="anchor" href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-8">Example on page 8<a class="anchor" aria-label="anchor" href="#example-on-page-8"></a> +</h3> +<p>For this dataset, the IORE fit does not converge when the default +starting values used by mkin for the IORE model are used. Therefore, a +lower value for the rate constant is used here.</p> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></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="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 1996.9408 444.9237 547.5616 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 477.4924</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span> +<span><span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span></span> +<span><span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span></span> +<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 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span> +<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span> +<span><span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span> +<span><span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</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 95.70619 8.99e-32 91.87941 99.53298</span></span> +<span><span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span></span> +<span><span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span></span> +<span><span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span></span> +<span><span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.3 287 86.3</span></span> +<span><span class="co">## IORE 53.4 668 201.0</span></span> +<span><span class="co">## DFOP 55.6 517 253.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 201.03</span></span></code></pre> +</div> +</div> +<div class="section level2"> +<h2 id="examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study<a class="anchor" aria-label="anchor" href="#examples-where-sfo-was-not-selected-for-an-abiotic-study"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a> +</h3> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></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="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 839.35238 88.57064 9.93363 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 105.5678</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span></span> +<span><span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span></span> +<span><span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span></span> +<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 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span> +<span><span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span> +<span><span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</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 9.85e+01 2.54e-20 97.390 99.672</span></span> +<span><span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span></span> +<span><span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span></span> +<span><span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span></span> +<span><span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 7.68e+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> +<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 class="section level3"> +<h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a> +</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">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 35.64867 23.22334 35.64867 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 28.54188</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span></span> +<span><span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span></span> +<span><span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span></span> +<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 93.863 2.32e-18 92.4565 95.269</span></span> +<span><span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span></span> +<span><span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span></span> +<span><span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</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 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 2.24e-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> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 17.8 59.2 17.8</span></span> +<span><span class="co">## IORE 18.4 49.2 14.8</span></span> +<span><span class="co">## DFOP 17.8 59.2 17.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 14.8</span></span></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 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="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_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="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="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> +<span><span class="co">## 899.4089 336.4348 899.4089 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 413.4841</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span> +<span><span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span></span> +<span><span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span></span> +<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 96.86 3.32e-12 90.848 102.863</span></span> +<span><span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span></span> +<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 111.810</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> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 14.0 46.5 14.00</span></span> +<span><span class="co">## IORE 16.4 29.4 8.86</span></span> +<span><span class="co">## DFOP 14.0 46.5 14.00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.86</span></span></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> +<div class="section level2"> +<h2 id="the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study<a class="anchor" aria-label="anchor" href="#the-dt50-was-not-observed-during-the-study"></a> +</h2> +<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="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="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="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> +<span><span class="co">## 579.6805 204.7932 144.7783 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 251.6944</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span> +<span><span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span></span> +<span><span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span></span> +<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 1.05e+02 NA 9.90e+01 1.10e+02</span></span> +<span><span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span></span> +<span><span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span></span> +<span><span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</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 1.05e+02 9.47e-13 99.9990 109.1224</span></span> +<span><span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span></span> +<span><span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span></span> +<span><span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span></span> +<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span> +<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] 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> +</div> +</div> +<div class="section level2"> +<h2 id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate +constant<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant"></a> +</h2> +<p>In the following three examples, the same results are obtained with +mkin as reported for PestDF. As in the case on page 10, the N values +below 1 are deemed unrealistic and appear to be the result of an +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="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_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="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="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> +<span><span class="co">## 695.4440 220.0685 695.4440 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 270.4679</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span></span> +<span><span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span></span> +<span><span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span></span> +<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 96.823 NA NA NA</span></span> +<span><span class="co">## k__iore_parent 2.436 NA NA NA</span></span> +<span><span class="co">## N_parent 0.263 NA NA NA</span></span> +<span><span class="co">## sigma 3.965 NA NA NA</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_0 100.521 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 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> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 5.58 18.5 5.58</span></span> +<span><span class="co">## IORE 6.49 13.2 3.99</span></span> +<span><span class="co">## DFOP 5.58 18.5 5.58</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 3.99</span></span></code></pre> +</div> +<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="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 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="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="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> +<span><span class="co">## 58.90242 19.06353 58.90242 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 51.51756</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span></span> +<span><span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span></span> +<span><span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span></span> +<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 95.523 0.0055 74.539157 116.51</span></span> +<span><span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span></span> +<span><span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span></span> +<span><span class="co">## sigma 1.953 0.0975 -5.893100 9.80</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 97.6840 NaN NaN NaN</span></span> +<span><span class="co">## k1 0.0589 NaN NA NA</span></span> +<span><span class="co">## k2 0.0589 NaN NA NA</span></span> +<span><span class="co">## g 0.6473 NaN NA NA</span></span> +<span><span class="co">## sigma 3.4323 NaN NaN NaN</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 11.8 39.1 11.80</span></span> +<span><span class="co">## IORE 12.9 31.4 9.46</span></span> +<span><span class="co">## DFOP 11.8 39.1 11.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 9.46</span></span></code></pre> +</div> +<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="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="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="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> +<span><span class="co">## 174.5971 142.3951 174.5971 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 172.131</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span> +<span><span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span></span> +<span><span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span></span> +<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 91.6016 6.34e-16 88.53086 94.672</span></span> +<span><span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span></span> +<span><span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span></span> +<span><span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> +<span><span class="co">## k1 0.00258 NA 4.18e-04 0.01592</span></span> +<span><span class="co">## k2 0.00258 NA 1.75e-03 0.00381</span></span> +<span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> +<span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 269 892 269</span></span> +<span><span class="co">## IORE 261 560 169</span></span> +<span><span class="co">## DFOP 269 892 269</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 168.51</span></span></code></pre> +</div> +</div> +<div class="section level2"> +<h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> +</h2> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$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="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="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> +<span><span class="co">## 48.43249 28.67746 27.26248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 32.83337</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span> +<span><span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span></span> +<span><span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span></span> +<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 1.00e+02 NA NaN NaN</span></span> +<span><span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span></span> +<span><span class="co">## N_parent 3.31e+00 NA NaN NaN</span></span> +<span><span class="co">## sigma 1.20e+00 NA 0.796 1.6</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 1.00e+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 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> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<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 3.55e+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> +<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 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="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="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="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> +<span><span class="co">## 245.5248 135.0132 245.5248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 165.9335</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span> +<span><span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span></span> +<span><span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span></span> +<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 95.874 2.94e-15 92.937 98.811</span></span> +<span><span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span></span> +<span><span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span></span> +<span><span class="co">## sigma 3.105 1.78e-04 1.795 4.416</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 97.96751 2.85e-13 94.21913 101.7159</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> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 72.8 242 72.8</span></span> +<span><span class="co">## IORE 76.3 137 41.3</span></span> +<span><span class="co">## DFOP 72.8 242 72.8</span></span> +<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="cb97"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="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="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> +<span><span class="co">## 106.91629 68.55574 106.91629 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 84.25618</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span> +<span><span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span></span> +<span><span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span></span> +<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 97.51348 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 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> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 143 474 143.0</span></span> +<span><span class="co">## IORE 131 236 71.2</span></span> +<span><span class="co">## DFOP 143 474 143.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 71.18</span></span></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 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="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="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="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> +<span><span class="co">## 3831.804 2062.008 1550.980 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 2247.348</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span></span> +<span><span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span></span> +<span><span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span></span> +<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 8.74e+01 2.48e-16 7.72e+01 97.52972</span></span> +<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span></span> +<span><span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span></span> +<span><span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</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 88.5333 7.40e-18 79.9836 97.083</span></span> +<span><span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span></span> +<span><span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span></span> +<span><span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 4.35 14.4 4.35</span></span> +<span><span class="co">## IORE 1.48 32.1 9.67</span></span> +<span><span class="co">## DFOP 0.67 21.4 8.93</span></span> +<span><span class="co">## </span></span> +<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 +<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> +</h2> +<p>The results obtained with mkin deviate from the results obtained with +PestDF either in cases where one of the interpretive rules would apply, +i.e. the IORE parameter N is less than one or the DFOP k values obtained +with PestDF are equal to the SFO k values, or in cases where the DFOP +model did not converge, which often lead to negative rate constants +returned by PestDF.</p> +<p>Therefore, mkin appears to suitable for kinetic evaluations according +to the NAFTA guidance.</p> +</div> +<div class="section level2"> +<h2 class="unnumbered" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> +<div id="refs" class="references csl-bib-body hanging-indent"> +<div id="ref-usepa2015" class="csl-entry"> +US EPA. 2015. <span>“Standard Operating Procedure for Using the NAFTA +Guidance to Calculate Representative Half-Life Values and Characterizing +Pesticide Degradation.”</span> <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a>. +</div> +</div> +</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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> 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aria-labelledby="dropdown-articles"> +<li><a class="dropdown-item" href="../../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> 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class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul> +</div> + + + </div> +</nav><div class="container template-article"> + + + + +<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 2025-02-14)</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="d-none name"><code>benchmarks.rmd</code></div> + </div> + + + +<p>Each system is characterized by the operating system type, the CPU +type, the mkin version, and, as in June 2022 the current R version lead +to worse performance, the R version. A compiler was available, so if no +analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks +is limited.</p> +<p>The following wrapper function for <code>mmkin</code> is used because +the way the error model is specified was changed in mkin version +0.9.49.1.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html" class="external-link">packageVersion</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span> <span class="op">></span> <span class="st">"0.9.48.1"</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="st">"const"</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, error_model <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span> <span class="op">}</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">mmkin_bench</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, <span class="va">error_model</span> <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, reweight.method <span class="op">=</span> <span class="va">error_model</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span> <span class="op">}</span></span> +<span><span class="op">}</span></span></code></pre></div> +<div class="section level2"> +<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> +</h2> +<p>Parent only:</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span></span> +<span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span> +<span><span class="va">parent_datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</span></span> +<span></span> +<span></span> +<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +<p>One metabolite:</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <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">"m1"</span><span class="op">)</span>,</span> +<span> m1 <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="op">)</span><span class="op">)</span></span> +<span><span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> m1 <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="op">)</span><span class="op">)</span></span> +<span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, <span class="co"># erroneously used FOMC twice, not fixed for consistency</span></span> +<span> m1 <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="op">)</span><span class="op">)</span></span> +<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +<p>Two metabolites, synthetic data:</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <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">"M1"</span><span class="op">)</span>,</span> +<span> M1 <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">"M2"</span><span class="op">)</span>,</span> +<span> M2 <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="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> M1 <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="op">)</span>,</span> +<span> M2 <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="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">SFO_lin_a</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span></span> +<span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span></span> +<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_lin_a</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span></span> +<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_lin_a</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span></span> +<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">SFO_lin_a</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> +</h2> +<p>Benchmarks for all available error models are shown. They are +intended for improving mkin, not for comparing CPUs or operating +systems. All trademarks belong to their respective owners.</p> +<div class="section level3"> +<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> +</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 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> +<th align="left">R</th> +<th align="left">mkin</th> +<th align="right">t1</th> +<th align="right">t2</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.48.1</td> +<td align="right">3.610</td> +<td align="right">11.019</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.1</td> +<td align="right">8.184</td> +<td align="right">22.889</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.2</td> +<td align="right">7.064</td> +<td align="right">12.558</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.3</td> +<td align="right">7.296</td> +<td align="right">21.239</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.4</td> +<td align="right">5.936</td> +<td align="right">20.545</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.2</td> +<td align="right">1.714</td> +<td align="right">3.971</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.3</td> +<td align="right">1.752</td> +<td align="right">4.156</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.4</td> +<td align="right">1.786</td> +<td align="right">3.729</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.3</td> +<td align="right">1.881</td> +<td align="right">3.504</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.4</td> +<td align="right">1.867</td> +<td align="right">3.450</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">1.791</td> +<td align="right">3.289</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">1.842</td> +<td align="right">3.453</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">1.959</td> +<td align="right">4.116</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">1.877</td> +<td align="right">3.906</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">1.644</td> +<td align="right">3.172</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">1.770</td> +<td align="right">3.377</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.2</td> +<td align="right">1.957</td> +<td align="right">3.633</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">2.140</td> +<td align="right">3.774</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">2.187</td> +<td align="right">3.851</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.288</td> +<td align="right">1.794</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.276</td> +<td align="right">1.804</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">1.370</td> +<td align="right">1.883</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">1.406</td> +<td align="right">1.948</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">1.386</td> +<td align="right">1.960</td> +</tr> +<tr class="odd"> +<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">1.2.5</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">1.371</td> +<td align="right">1.980</td> +</tr> +</tbody> +</table> +</div> +<div class="section level3"> +<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> +</h3> +<p>Constant variance (t3), two-component error model (t4), and variance +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> +<th align="left">R</th> +<th align="left">mkin</th> +<th align="right">t3</th> +<th align="right">t4</th> +<th align="right">t5</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.48.1</td> +<td align="right">3.764</td> +<td align="right">14.347</td> +<td align="right">9.495</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.1</td> +<td align="right">4.649</td> +<td align="right">13.789</td> +<td align="right">6.395</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.2</td> +<td align="right">4.786</td> +<td align="right">8.461</td> +<td align="right">5.675</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.3</td> +<td align="right">4.510</td> +<td align="right">13.805</td> +<td align="right">7.386</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.4</td> +<td align="right">4.446</td> +<td align="right">15.335</td> +<td align="right">6.002</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.2</td> +<td align="right">1.402</td> +<td align="right">6.174</td> +<td align="right">2.764</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.3</td> +<td align="right">1.430</td> +<td align="right">6.615</td> +<td align="right">2.878</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.4</td> +<td align="right">1.397</td> +<td align="right">7.251</td> +<td align="right">2.810</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.3</td> +<td align="right">1.430</td> +<td align="right">6.344</td> +<td align="right">2.798</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.4</td> +<td align="right">1.415</td> +<td align="right">6.364</td> +<td align="right">2.820</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">1.310</td> +<td align="right">6.279</td> +<td align="right">2.681</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">3.802</td> +<td align="right">21.247</td> +<td align="right">8.461</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">3.334</td> +<td align="right">19.521</td> +<td align="right">7.565</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">1.578</td> +<td align="right">8.058</td> +<td align="right">3.339</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">1.230</td> +<td align="right">5.839</td> +<td align="right">2.444</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">1.308</td> +<td align="right">5.758</td> +<td align="right">2.558</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.2</td> +<td align="right">1.503</td> +<td align="right">6.147</td> +<td align="right">2.803</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.554</td> +<td align="right">6.193</td> +<td align="right">2.843</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.585</td> +<td align="right">6.335</td> +<td align="right">3.003</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.792</td> +<td align="right">2.378</td> +<td align="right">1.245</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.784</td> +<td align="right">2.355</td> +<td align="right">1.233</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.770</td> +<td align="right">2.011</td> +<td align="right">1.123</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">0.793</td> +<td align="right">2.109</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">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.779</td> +<td align="right">2.080</td> +<td align="right">1.106</td> +</tr> +<tr class="odd"> +<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">1.2.5</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">0.762</td> +<td align="right">2.179</td> +<td align="right">1.131</td> +</tr> +</tbody> +</table> +</div> +<div class="section level3"> +<h3 id="two-metabolites">Two metabolites<a class="anchor" aria-label="anchor" href="#two-metabolites"></a> +</h3> +<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 style="width:100%;" class="table"> +<colgroup> +<col width="5%"> +<col width="40%"> +<col width="5%"> +<col width="8%"> +<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> +<th align="left">CPU</th> +<th align="left">R</th> +<th align="left">mkin</th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +<th align="right">t9</th> +<th align="right">t10</th> +<th align="right">t11</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.48.1</td> +<td align="right">2.623</td> +<td align="right">4.587</td> +<td align="right">7.525</td> +<td align="right">16.621</td> +<td align="right">8.576</td> +<td align="right">31.267</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.1</td> +<td align="right">2.542</td> +<td align="right">4.128</td> +<td align="right">4.632</td> +<td align="right">8.171</td> +<td align="right">3.676</td> +<td align="right">5.636</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.2</td> +<td align="right">2.723</td> +<td align="right">4.478</td> +<td align="right">4.862</td> +<td align="right">7.618</td> +<td align="right">3.579</td> +<td align="right">5.574</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.3</td> +<td align="right">2.643</td> +<td align="right">4.374</td> +<td align="right">7.020</td> +<td align="right">11.124</td> +<td align="right">5.388</td> +<td align="right">7.365</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.49.4</td> +<td align="right">2.635</td> +<td align="right">4.259</td> +<td align="right">4.737</td> +<td align="right">7.763</td> +<td align="right">3.427</td> +<td align="right">5.626</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.2</td> +<td align="right">0.777</td> +<td align="right">1.236</td> +<td align="right">1.332</td> +<td align="right">2.872</td> +<td align="right">2.069</td> +<td align="right">2.987</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.3</td> +<td align="right">0.858</td> +<td align="right">1.264</td> +<td align="right">1.333</td> +<td align="right">2.984</td> +<td align="right">2.113</td> +<td align="right">3.073</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">0.9.50.4</td> +<td align="right">0.783</td> +<td align="right">1.282</td> +<td align="right">1.486</td> +<td align="right">3.815</td> +<td align="right">1.958</td> +<td align="right">3.105</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.3</td> +<td align="right">0.763</td> +<td align="right">1.244</td> +<td align="right">1.457</td> +<td align="right">3.054</td> +<td align="right">1.923</td> +<td align="right">2.839</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">NA</td> +<td align="left">1.0.4</td> +<td align="right">0.785</td> +<td align="right">1.252</td> +<td align="right">1.466</td> +<td align="right">3.091</td> +<td align="right">1.936</td> +<td align="right">2.826</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">0.744</td> +<td align="right">1.227</td> +<td align="right">1.288</td> +<td align="right">3.553</td> +<td align="right">1.895</td> +<td align="right">2.738</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">3.018</td> +<td align="right">4.165</td> +<td align="right">5.036</td> +<td align="right">10.844</td> +<td align="right">6.623</td> +<td align="right">9.722</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.0</td> +<td align="right">2.522</td> +<td align="right">3.792</td> +<td align="right">4.143</td> +<td align="right">11.268</td> +<td align="right">5.935</td> +<td align="right">8.728</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.1.3</td> +<td align="left">1.1.0</td> +<td align="right">0.907</td> +<td align="right">1.535</td> +<td align="right">1.589</td> +<td align="right">4.544</td> +<td align="right">2.302</td> +<td align="right">3.463</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">i7-4710MQ</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">0.678</td> +<td align="right">1.095</td> +<td align="right">1.149</td> +<td align="right">3.247</td> +<td align="right">1.658</td> +<td align="right">2.472</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.1</td> +<td align="right">0.696</td> +<td align="right">1.124</td> +<td align="right">1.321</td> +<td align="right">2.786</td> +<td align="right">1.744</td> +<td align="right">2.566</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.1</td> +<td align="left">1.1.2</td> +<td align="right">0.861</td> +<td align="right">1.295</td> +<td align="right">1.507</td> +<td align="right">3.102</td> +<td align="right">1.961</td> +<td align="right">2.852</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.913</td> +<td align="right">1.345</td> +<td align="right">1.539</td> +<td align="right">3.011</td> +<td align="right">1.987</td> +<td align="right">2.802</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.935</td> +<td align="right">1.381</td> +<td align="right">1.551</td> +<td align="right">3.209</td> +<td align="right">1.976</td> +<td align="right">3.013</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.445</td> +<td align="right">0.591</td> +<td align="right">0.660</td> +<td align="right">1.190</td> +<td align="right">0.814</td> +<td align="right">1.100</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.443</td> +<td align="right">0.586</td> +<td align="right">0.661</td> +<td align="right">1.176</td> +<td align="right">0.803</td> +<td align="right">1.097</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.2</td> +<td align="left">1.2.3</td> +<td align="right">0.418</td> +<td align="right">0.530</td> +<td align="right">0.591</td> +<td align="right">1.006</td> +<td align="right">0.716</td> +<td align="right">0.949</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.2.3</td> +<td align="left">1.2.3</td> +<td align="right">0.432</td> +<td align="right">0.549</td> +<td align="right">0.609</td> +<td align="right">1.052</td> +<td align="right">0.743</td> +<td align="right">0.989</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.410</td> +<td align="right">0.526</td> +<td align="right">0.553</td> +<td align="right">1.249</td> +<td align="right">0.712</td> +<td align="right">0.948</td> +</tr> +<tr class="odd"> +<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">1.2.5</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">0.426</td> +<td align="right">0.533</td> +<td align="right">0.565</td> +<td align="right">1.296</td> +<td align="right">0.728</td> +<td align="right">0.978</td> +</tr> +</tbody> +</table> +</div> +</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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> +</html> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html new file mode 100644 index 00000000..113f7b67 --- /dev/null +++ b/docs/dev/articles/web_only/compiled_models.html @@ -0,0 +1,231 @@ +<!DOCTYPE html> +<!-- 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title="In-development version">1.2.10</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> + + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"> +<li class="nav-item"><a class="nav-link" href="../../reference/index.html">Reference</a></li> +<li class="active nav-item dropdown"> + <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"> +<li><a class="dropdown-item" href="../../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul> +</li> +<li class="nav-item"><a class="nav-link" href="../../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../../news/index.html">News</a></li> + </ul> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul> +</div> + + + </div> +</nav><div class="container template-article"> + + + + +<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">2025-02-14</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="d-none name"><code>compiled_models.rmd</code></div> + </div> + + + +<div class="section level2"> +<h2 id="how-to-benefit-from-compiled-models">How to benefit from compiled models<a class="anchor" aria-label="anchor" href="#how-to-benefit-from-compiled-models"></a> +</h2> +<p>When using an mkin version equal to or greater than 0.9-36 and a C +compiler is available, you will see a message that the model is being +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://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 +gcc or clang installed. On Debian based linux distributions, these will +be pulled in by installing the build-essential package.</p> +<p>On MacOS, which I do not use personally, I have had reports that a +compiler is available by default.</p> +<p>On Windows, you need to install Rtools and have the path to its bin +directory in your PATH variable. You do not need to modify the PATH +variable when installing Rtools. Instead, I would recommend to put the +line</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>PATH <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"C:/Rtools/bin"</span>, <span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"PATH"</span><span class="op">)</span>, sep<span class="op">=</span><span class="st">";"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p>into your .Rprofile startup file. This is just a text file with some +R code that is executed when your R session starts. It has to be named +.Rprofile and has to be located in your home directory, which will +generally be your Documents folder. You can check the location of the +home directory used by R by issuing</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"HOME"</span><span class="op">)</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="comparison-with-other-solution-methods">Comparison with other solution methods<a class="anchor" aria-label="anchor" href="#comparison-with-other-solution-methods"></a> +</h2> +<p>First, we build a simple degradation model for a parent compound with +one metabolite, and we remove zero values from the dataset.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="st"><a href="https://pkgdown.jrwb.de/mkin/">"mkin"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <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">"m1"</span><span class="op">)</span>,</span> +<span> m1 <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="op">)</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> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></code></pre></div> +<p>We can compare the performance of the Eigenvalue based solution +against the compiled version and the R implementation of the +differential equations using the benchmark package. In the output of +below code, the warnings about zero being removed from the FOCUS D +dataset are suppressed. Since mkin version 0.9.49.11, an analytical +solution is also implemented, which is included in the tests below.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"Eigenvalue based"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"eigen"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"analytical"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span> +<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</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">b.1</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</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="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 0.102</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.324 0.135</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.706 0.174</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 22.627 2.308</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> +<div class="section level2"> +<h2 id="model-without-analytical-solution">Model without analytical solution<a class="anchor" aria-label="anchor" href="#model-without-analytical-solution"></a> +</h2> +<p>This evaluation is also taken from the example section of mkinfit. No +analytical solution is available for this system, and now Eigenvalue +based solution is possible, so only deSolve using with or without +compiled code is available.</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> m1 <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="op">)</span><span class="op">)</span></span> +<span></span> +<span> <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>,</span> +<span> use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> +<span> replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>,</span> +<span> columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</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">b.2</span><span class="op">)</span></span> +<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="va">b.2</span><span class="op">[</span><span class="st">"1"</span>, <span class="st">"relative"</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</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="st">"R package benchmark is not available"</span><span class="op">)</span></span> +<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 0.170</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.865 4.057</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 1.2.10 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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> +</div> + + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> +</html> diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html new file mode 100644 index 00000000..572f253d --- /dev/null +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -0,0 +1,651 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<title>Example evaluations of the dimethenamid data from 2018 • mkin</title> +<script src="../../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, 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data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"> +<li><a class="dropdown-item" href="../../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart 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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="d-none name"><code>dimethenamid_2018.rmd</code></div> + </div> + + + +<p><a href="http://www.jrwb.de" class="external-link">Wissenschaftlicher Berater, Kronacher +Str. 12, 79639 Grenzach-Wyhlen, Germany</a></p> +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> +<p>A first analysis of the data analysed here was presented in a recent +journal article on nonlinear mixed-effects models in degradation +kinetics <span class="citation">(Ranke et al. 2021)</span>. That +analysis was based on the <code>nlme</code> package and a development +version of the <code>saemix</code> package that was unpublished at the +time. Meanwhile, version 3.0 of the <code>saemix</code> package is +available from the CRAN repository. Also, it turned out that there was +an error in the handling of the Borstel data in the mkin package at the +time, leading to the duplication of a few data points from that soil. +The dataset in the mkin package has been corrected, and the interface to +<code>saemix</code> in the mkin package has been updated to use the +released version.</p> +<p>This vignette is intended to present an up to date analysis of the +data, using the corrected dataset and released versions of +<code>mkin</code> and <code>saemix</code>.</p> +</div> +<div class="section level2"> +<h2 id="data">Data<a class="anchor" aria-label="anchor" href="#data"></a> +</h2> +<p>Residue data forming the basis for the endpoints derived in the +conclusion on the peer review of the pesticide risk assessment of +dimethenamid-P published by the European Food Safety Authority (EFSA) in +2018 <span class="citation">(EFSA 2018)</span> were transcribed from the +risk assessment report <span class="citation">(Rapporteur Member State +Germany, Co-Rapporteur Member State Bulgaria 2018)</span> which can be +downloaded from the Open EFSA repository <a href="https://open.efsa.europa.eu" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a>.</p> +<p>The data are <a href="https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html">available +in the mkin package</a>. The following code (hidden by default, please +use the button to the right to show it) treats the data available for +the racemic mixture dimethenamid (DMTA) and its enantiomer +dimethenamid-P (DMTAP) in the same way, as no difference between their +degradation behaviour was identified in the EU risk assessment. The +observation times of each dataset are multiplied with the corresponding +normalisation factor also available in the dataset, in order to make it +possible to describe all datasets with a single set of parameters.</p> +<p>Also, datasets observed in the same soil are merged, resulting in +dimethenamid (DMTA) data from six soils.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="parent-degradation">Parent degradation<a class="anchor" aria-label="anchor" href="#parent-degradation"></a> +</h2> +<p>We evaluate the observed degradation of the parent compound using +simple exponential decline (SFO) and biexponential decline (DFOP), using +constant variance (const) and a two-component variance (tc) as error +models.</p> +<div class="section level3"> +<h3 id="separate-evaluations">Separate evaluations<a class="anchor" aria-label="anchor" href="#separate-evaluations"></a> +</h3> +<p>As a first step, to get a visual impression of the fit of the +different models, we do separate evaluations for each soil using the +mmkin function from the mkin package:</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_mkin_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">dmta_ds</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">f_parent_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">dmta_ds</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<p>The plot of the individual SFO fits shown below suggests that at +least in some datasets the degradation slows down towards later time +points, and that the scatter of the residuals error is smaller for +smaller values (panel to the right):</p> +<div class="sourceCode" id="cb3"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> +<p>Using biexponential decline (DFOP) results in a slightly more random +scatter of the residuals:</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> +<p>The population curve (bold line) in the above plot results from +taking the mean of the individual transformed parameters, i.e. of log k1 +and log k2, as well as of the logit of the g parameter of the DFOP +model). Here, this procedure does not result in parameters that +represent the degradation well, because in some datasets the fitted +value for k2 is extremely close to zero, leading to a log k2 value that +dominates the average. This is alleviated if only rate constants that +pass the t-test for significant difference from zero (on the +untransformed scale) are considered in the averaging:</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> +<p>While this is visually much more satisfactory, such an average +procedure could introduce a bias, as not all results from the individual +fits enter the population curve with the same weight. This is where +nonlinear mixed-effects models can help out by treating all datasets +with equally by fitting a parameter distribution model together with the +degradation model and the error model (see below).</p> +<p>The remaining trend of the residuals to be higher for higher +predicted residues is reduced by using the two-component error +model:</p> +<div class="sourceCode" id="cb6"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> +<p>However, note that in the case of using this error model, the fits to +the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by +the fact that they did not converge:</p> +<div class="sourceCode" id="cb7"><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">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><mmkin> object +Status of individual fits: + + dataset +model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot + DFOP OK OK OK OK C OK + +C: Optimisation did not converge: +iteration limit reached without convergence (10) +OK: No warnings</code></pre> +</div> +<div class="section level3"> +<h3 id="nonlinear-mixed-effects-models">Nonlinear mixed-effects models<a class="anchor" aria-label="anchor" href="#nonlinear-mixed-effects-models"></a> +</h3> +<p>Instead of taking a model selection decision for each of the +individual fits, we fit nonlinear mixed-effects models (using different +fitting algorithms as implemented in different packages) and do model +selection using all available data at the same time. In order to make +sure that these decisions are not unduly influenced by the type of +algorithm used, by implementation details or by the use of wrong control +parameters, we compare the model selection results obtained with +different R packages, with different algorithms and checking control +parameters.</p> +<div class="section level4"> +<h4 id="nlme">nlme<a class="anchor" aria-label="anchor" href="#nlme"></a> +</h4> +<p>The nlme package was the first R extension providing facilities to +fit nonlinear mixed-effects models. We would like to do model selection +from all four combinations of degradation models and error models based +on the AIC. However, fitting the DFOP model with constant variance and +using default control parameters results in an error, signalling that +the maximum number of 50 iterations was reached, potentially indicating +overparameterisation. Nevertheless, the algorithm converges when the +two-component error model is used in combination with the DFOP model. +This can be explained by the fact that the smaller residues observed at +later sampling times get more weight when using the two-component error +model which will counteract the tendency of the algorithm to try +parameter combinations unsuitable for fitting these data.</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> +<span><span class="va">f_parent_nlme_sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span><span class="co"># f_parent_nlme_dfop_const <- nlme(f_parent_mkin_const["DFOP", ])</span></span> +<span><span class="va">f_parent_nlme_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> +<span><span class="va">f_parent_nlme_dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></code></pre></div> +<p>Note that a certain degree of overparameterisation is also indicated +by a warning obtained when fitting DFOP with the two-component error +model (‘false convergence’ in the ‘LME step’ in iteration 3). However, +as this warning does not occur in later iterations, and specifically not +in the last of the 5 iterations, we can ignore this warning.</p> +<p>The model comparison function of the nlme package can directly be +applied to these fits showing a much lower AIC for the DFOP model fitted +with the two-component error model. Also, the likelihood ratio test +indicates that this difference is significant as the p-value is below +0.0001.</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">f_parent_nlme_sfo_const</span>, <span class="va">f_parent_nlme_sfo_tc</span>, <span class="va">f_parent_nlme_dfop_tc</span></span> +<span><span class="op">)</span></span></code></pre></div> +<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 -325.95 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 +attempts can be made visible below.</p> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_nlme_sfo_const_logchol</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>,</span> +<span> random <span class="op">=</span> <span class="fu">nlme</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdLogChol.html" class="external-link">pdLogChol</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DMTA_0</span> <span class="op">~</span> <span class="fl">1</span>, <span class="va">log_k_DMTA</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_parent_nlme_sfo_const</span>, <span class="va">f_parent_nlme_sfo_const_logchol</span><span class="op">)</span></span> +<span><span class="va">f_parent_nlme_sfo_tc_logchol</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>,</span> +<span> random <span class="op">=</span> <span class="fu">nlme</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdLogChol.html" class="external-link">pdLogChol</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DMTA_0</span> <span class="op">~</span> <span class="fl">1</span>, <span class="va">log_k_DMTA</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_parent_nlme_sfo_tc</span>, <span class="va">f_parent_nlme_sfo_tc_logchol</span><span class="op">)</span></span> +<span><span class="va">f_parent_nlme_dfop_tc_logchol</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>,</span> +<span> random <span class="op">=</span> <span class="fu">nlme</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdLogChol.html" class="external-link">pdLogChol</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">DMTA_0</span> <span class="op">~</span> <span class="fl">1</span>, <span class="va">log_k1</span> <span class="op">~</span> <span class="fl">1</span>, <span class="va">log_k2</span> <span class="op">~</span> <span class="fl">1</span>, <span class="va">g_qlogis</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span>, <span class="va">f_parent_nlme_dfop_tc_logchol</span><span class="op">)</span></span></code></pre></div> +<p>While the SFO variants converge fast, the additional parameters +introduced by this lead to convergence warnings for the DFOP model. The +model comparison clearly show that adding correlations between random +effects does not improve the fits.</p> +<p>The selected model (DFOP with two-component error) fitted to the data +assuming no correlations between random effects is shown below.</p> +<div class="sourceCode" id="cb13"><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">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> +</div> +<div class="section level4"> +<h4 id="saemix">saemix<a class="anchor" aria-label="anchor" href="#saemix"></a> +</h4> +<p>The saemix package provided the first Open Source implementation of +the Stochastic Approximation to the Expectation Maximisation (SAEM) +algorithm. SAEM fits of degradation models can be conveniently performed +using an interface to the saemix package available in current +development versions of the mkin package.</p> +<p>The corresponding SAEM fits of the four combinations of degradation +and error models are fitted below. As there is no convergence criterion +implemented in the saemix package, the convergence plots need to be +manually checked for every fit. We define control settings that work +well for all the parent data fits shown in this vignette.</p> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> +<span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span><span class="va">saemix_control_10k</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10000</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<p>The convergence plot for the SFO model using constant variance is +shown below.</p> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<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">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_const-1.png" width="700"></p> +<p>Obviously the selected number of iterations is sufficient to reach +convergence. This can also be said for the SFO fit using the +two-component error model.</p> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<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">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> +<p>When fitting the DFOP model with constant variance (see below), +parameter convergence is not as unambiguous.</p> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> +<div class="sourceCode" id="cb18"><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">f_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div> +<pre><code>Kinetic nonlinear mixed-effects model fit by SAEM +Structural model: +d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * DMTA + +Data: +155 observations of 1 variable(s) grouped in 6 datasets + +Likelihood computed by importance sampling + AIC BIC logLik + 706 704 -344 + +Fitted parameters: + estimate lower upper +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 1.60516 2.0377 +SD.DMTA_0 1.64787 0.45729 2.8384 +SD.k1 0.57439 0.24731 0.9015 +SD.k2 0.03296 -2.50524 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 +standard deviation of k2 across the population of soils +(<code>SD.k2</code>) is ill-defined, indicating overparameterisation of +this model.</p> +<p>When the DFOP model is fitted with the two-component error model, we +also observe that the estimated variance of k2 becomes very small, while +being ill-defined, as illustrated by the excessive confidence interval +of <code>SD.k2</code>.</p> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<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">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> +<p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> +<div class="sourceCode" id="cb21"><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">f_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code>Kinetic nonlinear mixed-effects model fit by SAEM +Structural model: +d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * + time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) + * DMTA + +Data: +155 observations of 1 variable(s) grouped in 6 datasets + +Likelihood computed by importance sampling + AIC BIC logLik + 666 664 -323 + +Fitted parameters: + 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 +an error message. This is related to the variance of k2 approximating +zero and has been submitted as a <a href="https://github.com/saemixdevelopment/saemixextension/issues/29" class="external-link">bug +to the saemix package</a>, as the algorithm does not converge in this +case.</p> +<p>An alternative way to fit DFOP in combination with the two-component +error model is to use the model formulation with transformed parameters +as used per default in mkin. When using this option, convergence is +slower, but eventually the algorithm stops as well with the same error +message.</p> +<p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and +the version with increased iterations can be compared using the model +comparison function of the saemix package:</p> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span></span> +<span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div> +<pre><code>Likelihoods calculated by importance sampling</code></pre> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> +<span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</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</span><span class="op">)</span></span></code></pre></div> +<pre><code> AIC BIC +SFO const 796.38 795.34 +SFO tc 798.38 797.13 +DFOP const 705.75 703.88 +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 +the three methods are compared.</p> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> +<span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> +<span><span class="va">AIC_parent_saemix_methods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> +<span> is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span>,</span> +<span> gq <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"gq"</span><span class="op">)</span>,</span> +<span> lin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"lin"</span><span class="op">)</span></span> +<span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> +<pre><code> is gq lin +665.67 665.74 665.13 </code></pre> +<p>The AIC values based on importance sampling and Gaussian quadrature +are very similar. Using linearisation is known to be less accurate, but +still gives a similar value.</p> +<p>In order to illustrate that the comparison of the three method +depends on the degree of convergence obtained in the fit, the same +comparison is shown below for the fit using the defaults for the number +of iterations and the number of MCMC chains.</p> +<p>When using OpenBlas for linear algebra, there is a large difference +in the values obtained with Gaussian quadrature, so the larger number of +iterations makes a lot of difference. When using the LAPACK version +coming with Debian Bullseye, the AIC based on Gaussian quadrature is +almost the same as the one obtained with the other methods, also when +using defaults for the fit.</p> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> +<span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> +<span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> +<span><span class="va">AIC_parent_saemix_methods_defaults</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> +<span> is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span>,</span> +<span> gq <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"gq"</span><span class="op">)</span>,</span> +<span> lin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span>, method <span class="op">=</span> <span class="st">"lin"</span><span class="op">)</span></span> +<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 +670.09 669.37 671.29 </code></pre> +</div> +</div> +<div class="section level3"> +<h3 id="comparison">Comparison<a class="anchor" aria-label="anchor" href="#comparison"></a> +</h3> +<p>The following table gives the AIC values obtained with both backend +packages using the same control parameters (800 iterations burn-in, 300 +iterations second phase, 15 chains).</p> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> <span class="st">"Degradation model"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> +<span> <span class="st">"Error model"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"const"</span>, <span class="st">"tc"</span>, <span class="st">"const"</span>, <span class="st">"tc"</span><span class="op">)</span>,</span> +<span> nlme <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_nlme_sfo_const</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_nlme_sfo_tc</span><span class="op">)</span>, <span class="cn">NA</span>, <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span><span class="op">)</span>,</span> +<span> saemix_lin <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"lin"</span><span class="op">)</span>,</span> +<span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> +<span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span> +<span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left">Degradation model</th> +<th align="left">Error model</th> +<th align="right">nlme</th> +<th align="right">saemix_lin</th> +<th align="right">saemix_is</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">const</td> +<td align="right">796.60</td> +<td align="right">796.60</td> +<td align="right">796.38</td> +</tr> +<tr class="even"> +<td align="left">SFO</td> +<td align="left">tc</td> +<td align="right">798.60</td> +<td align="right">798.60</td> +<td align="right">798.38</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">const</td> +<td align="right">NA</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">665.13</td> +<td align="right">665.67</td> +</tr> +</tbody> +</table> +</div> +</div> +<div class="section level2"> +<h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a> +</h2> +<p>A more detailed analysis of the dimethenamid dataset confirmed that +the DFOP model provides the most appropriate description of the decline +of the parent compound in these data. On the other hand, closer +inspection of the results revealed that the variability of the k2 +parameter across the population of soils is ill-defined. This coincides +with the observation that this parameter cannot robustly be quantified +for some of the soils.</p> +<p>Regarding the regulatory use of these data, it is claimed that an +improved characterisation of the mean parameter values across the +population is obtained using the nonlinear mixed-effects models +presented here. However, attempts to quantify the variability of the +slower rate constant of the biphasic decline of dimethenamid indicate +that the data are not sufficient to characterise this variability to a +satisfactory precision.</p> +</div> +<div class="section level2"> +<h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a> +</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 4.4.2 (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/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 + [3] LC_TIME=C LC_COLLATE=de_DE.UTF-8 + [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 + [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [9] LC_ADDRESS=C LC_TELEPHONE=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C + +time zone: Europe/Berlin +tzcode source: system (glibc) + +attached base packages: +[1] stats graphics grDevices utils datasets methods base + +other attached packages: +[1] saemix_3.3 npde_3.5 nlme_3.1-166 mkin_1.2.10 knitr_1.49 + +loaded via a namespace (and not attached): + [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] mclust_6.1.1 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1 +[41] glue_1.8.0 codetools_0.2-20 ragg_1.3.3 zoo_1.8-12 +[45] fansi_1.0.6 colorspace_2.1-1 rmarkdown_2.29 pkgconfig_2.0.3 +[49] 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> +</h2> +<!-- vim: set foldmethod=syntax: --> +<div id="refs" class="references csl-bib-body hanging-indent"> +<div id="ref-efsa_2018_dimethenamid" class="csl-entry"> +EFSA. 2018. <span>“Peer Review of the Pesticide Risk Assessment of the +Active Substance Dimethenamid-p.”</span> <em>EFSA Journal</em> 16: 5211. +</div> +<div id="ref-ranke2021" class="csl-entry"> +Ranke, Johannes, Janina Wöltjen, Jana Schmidt, and Emmanuelle Comets. +2021. <span>“Taking Kinetic Evaluations of Degradation Data to the Next +Level with Nonlinear Mixed-Effects Models.”</span> <em>Environments</em> +8 (8). <a href="https://doi.org/10.3390/environments8080071" class="external-link">https://doi.org/10.3390/environments8080071</a>. +</div> +<div id="ref-dimethenamid_rar_2018_b8" class="csl-entry"> +Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria. +2018. <span>“<span class="nocase">Renewal Assessment Report +Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour, Rev. 2 - +November 2017</span>.”</span> <a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a>. +</div> +</div> +</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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> 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fa-lg"></span></a></li> + </ul> +</div> + + + </div> +</nav><div class="container template-article"> + + + + +<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 2025-02-14)</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="d-none name"><code>multistart.rmd</code></div> + </div> + + + +<p>The dimethenamid data from 2018 from seven soils is used as example +data in this vignette.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +<p>First, we check the DFOP model with the two-component error model and +random effects for all degradation parameters.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<p>We see that not all variability parameters are identifiable. The +<code>illparms</code> function tells us that the confidence interval for +the standard deviation of ‘log_k2’ includes zero. We check this +assessment using multiple runs with different starting values.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p> +<p>This confirms that the variance of k2 is the most problematic +parameter, so we reduce the parameter distribution model by removing the +intersoil variability for k2.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_reduced</span> <span class="op"><-</span> <span class="fu">stats</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> +<span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p> +<p>The results confirm that all remaining parameters can be determined +with sufficient certainty.</p> +<p>We can also analyse the log-likelihoods obtained in the multiple +runs:</p> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/llhist.html">llhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p> +<p>We can use the <code>anova</code> method to compare the models.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span>,</span> +<span> <span class="va">f_saem_reduced</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<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 9 663.67 661.80 -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> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> + </nav></aside> +</div> + + + + <footer><div class="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> +</html> diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png Binary files differnew file mode 100644 index 00000000..19b68cfe --- /dev/null +++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png 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L3</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul> +</li> +<li class="nav-item"><a class="nav-link" href="../../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../../news/index.html">News</a></li> + </ul> +<ul class="navbar-nav"> +<li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../../search.json"> +</form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> + </ul> +</div> + + + </div> +</nav><div class="container template-article"> + + + + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Benchmark timings for saem.mmkin</h1> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> + + <h4 data-toc-skip class="date">Last change 17 February 2023 +(rebuilt 2025-02-14)</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="d-none name"><code>saem_benchmarks.rmd</code></div> + </div> + + + +<p>Each system is characterized by operating system type, CPU type, mkin +version, saemix version and R version. A compiler was available, so if +no analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks +is limited.</p> +<p>For the initial mmkin fits, we use all available cores.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<div class="section level2"> +<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> +</h2> +<p>Please refer to the vignette <code>dimethenamid_2018</code> for an +explanation of the following preprocessing.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> +</h2> +<div class="section level3"> +<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> +</h3> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">parent_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> +<span><span class="va">parent_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="va">parent_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">sfo_const</td> +<td align="right">5</td> +<td align="right">796.3</td> +<td align="right">795.3</td> +<td align="right">-393.2</td> +</tr> +<tr class="even"> +<td align="left">sfo_tc</td> +<td align="right">6</td> +<td align="right">798.3</td> +<td align="right">797.1</td> +<td align="right">-393.2</td> +</tr> +<tr class="odd"> +<td align="left">dfop_const</td> +<td align="right">9</td> +<td align="right">709.4</td> +<td align="right">707.5</td> +<td align="right">-345.7</td> +</tr> +<tr class="even"> +<td align="left">sforb_const</td> +<td align="right">9</td> +<td align="right">710.0</td> +<td align="right">708.1</td> +<td align="right">-346.0</td> +</tr> +<tr class="odd"> +<td align="left">hs_const</td> +<td align="right">9</td> +<td align="right">713.7</td> +<td align="right">711.8</td> +<td align="right">-347.8</td> +</tr> +<tr class="even"> +<td align="left">dfop_tc</td> +<td align="right">10</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">662.9</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">667.2</td> +<td align="right">665.1</td> +<td align="right">-323.6</td> +</tr> +</tbody> +</table> +<p>The above model comparison suggests to use the SFORB model with +two-component error. For comparison, we keep the DFOP model with +two-component error, as it competes with SFORB for biphasic curves.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre> +<p>For these two models, random effects for the transformed parameters +<code>k2</code> and <code>k_DMTA_bound_free</code> could not be +quantified.</p> +</div> +<div class="section level3"> +<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> +</h3> +<p>We remove parameters that were found to be ill-defined in the parent +only fits.</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">one_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> +<span> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <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="op">)</span><span class="op">)</span>,</span> +<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <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="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">one_met_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">one_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +<div class="section level3"> +<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a> +</h3> +<p>For the case of three metabolites, we only keep the SFORB model in +order to limit the time for compiling this vignette, and as fitting in +parallel may disturb the benchmark. Again, we do not include random +effects that were ill-defined in previous fits of subsets of the +degradation model.</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">three_met_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> +<span> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> M23 <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="op">)</span>,</span> +<span> M27 <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="op">)</span>,</span> +<span> M31 <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">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">three_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +</div> +<div class="section level2"> +<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> +</h2> +<p>Benchmarks for all available error models are shown. They are +intended for improving mkin, not for comparing CPUs or operating +systems. All trademarks belong to their respective owners.</p> +<div class="section level3"> +<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> +</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> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t1</th> +<th align="right">t2</th> +<th align="right">t3</th> +<th align="right">t4</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">2.140</td> +<td align="right">4.626</td> +<td align="right">4.328</td> +<td align="right">4.998</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">2.427</td> +<td align="right">4.550</td> +<td align="right">4.217</td> +<td align="right">4.851</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">1.352</td> +<td align="right">2.813</td> +<td align="right">2.401</td> +<td align="right">2.074</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">1.328</td> +<td align="right">2.738</td> +<td align="right">2.336</td> +<td align="right">2.023</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">1.118</td> +<td align="right">2.036</td> +<td align="right">2.010</td> +<td align="right">2.088</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">1.419</td> +<td align="right">2.374</td> +<td align="right">1.926</td> +<td align="right">2.398</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">0.972</td> +<td align="right">2.550</td> +<td align="right">1.987</td> +<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">1.2.6</td> +<td align="left">3.2</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">2.277</td> +<td align="right">1.945</td> +<td align="right">2.134</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> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t5</th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">5.678</td> +<td align="right">7.441</td> +<td align="right">8.000</td> +<td align="right">7.980</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">5.352</td> +<td align="right">7.201</td> +<td align="right">8.174</td> +<td align="right">8.401</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">2.388</td> +<td align="right">3.033</td> +<td align="right">3.532</td> +<td align="right">3.310</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">2.341</td> +<td align="right">2.968</td> +<td align="right">3.465</td> +<td align="right">3.341</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">2.159</td> +<td align="right">3.584</td> +<td align="right">3.307</td> +<td align="right">3.460</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">2.348</td> +<td align="right">3.134</td> +<td align="right">3.253</td> +<td align="right">3.530</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">2.127</td> +<td align="right">3.587</td> +<td align="right">3.433</td> +<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">1.2.6</td> +<td align="left">3.2</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">2.372</td> +<td align="right">3.137</td> +<td align="right">3.100</td> +<td align="right">3.281</td> +</tr> +</tbody> +</table> +</div> +<div class="section level3"> +<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 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> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t9</th> +<th align="right">t10</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">24.465</td> +<td align="right">800.266</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">25.193</td> +<td align="right">798.580</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">11.247</td> +<td align="right">285.216</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">11.242</td> +<td align="right">284.258</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">11.796</td> +<td align="right">216.012</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">12.841</td> +<td align="right">292.688</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">12.160</td> +<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">1.2.6</td> +<td align="left">3.2</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">11.590</td> +<td align="right">279.782</td> +</tr> +</tbody> +</table> +</div> +<div class="section level3"> +<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a> +</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> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t11</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">1289.198</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">1312.445</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.1</td> +<td align="left">3.2</td> +<td align="right">489.939</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">482.970</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">392.364</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.3</td> +<td align="left">3.2</td> +<td align="right">483.027</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<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">1.2.6</td> +<td align="left">3.2</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">469.036</td> +</tr> +</tbody> +</table> +</div> +</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="pkgdown-footer-left"> + <p>Developed by Johannes Ranke.</p> +</div> + +<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> +</div> + + + + + + </body> +</html> |
