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<h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
<h4 data-toc-skip class="date">Last change 16 January 2018
(rebuilt 2023-05-19)</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small>
<div class="hidden name"><code>FOCUS_Z.rmd</code></div>
</div>
<p><a href="http://www.jrwb.de" 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 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span>
<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span>
<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span>
<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span>
<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span>
<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span>
<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co">## $ff</span></span>
<span><span class="co">## Z2_Z3 Z2_sink </span></span>
<span><span class="co">## 0.4715 0.5285 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## $distimes</span></span>
<span><span class="co">## DT50 DT90</span></span>
<span><span class="co">## Z0 0.31288 1.0394</span></span>
<span><span class="co">## Z1 1.44917 4.8141</span></span>
<span><span class="co">## Z2 1.53478 5.0984</span></span>
<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre>
<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 <span class="math inline">\(\chi^2\)</span> error level is
lower for metabolite Z3 using this model and the graphical fit for Z3 is
improved. However, the covariance matrix is not returned.</p>
<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">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span>
<span><span class="co">## </span></span>
<span><span class="co">## $distimes</span></span>
<span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span>
<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span>
<span><span class="co">## 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>
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