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diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html new file mode 100644 index 00000000..7b54053f --- /dev/null +++ b/docs/dev/reference/schaefer07_complex_case.html @@ -0,0 +1,175 @@ +<!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>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link 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class="page-header"> + + <h1>Metabolism data set used for checking the software quality of KinGUI</h1> + + <div class="d-none name"><code>schaefer07_complex_case.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the + software quality of KinGUI in the original publication (Schäfer et al., 2007). + The results from the fitting are also included.</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> + <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl><dt><code>time</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>parent</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>A1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>B1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>C1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>A2</code></dt> +<dd><p>a numeric vector</p></dd> + + +</dl><p>The results are a data frame with 14 results for different parameter values</p> + </div> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> + <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic + software tool for evaluations according to FOCUS degradation kinetics. In: Del + Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII + Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> + </div> + + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <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>type <span class="op">=</span> <span class="st">"SFO"</span>, to <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">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <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>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> B1 <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>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> C1 <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>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <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>type <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></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><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">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="schaefer07_complex_case-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.3809618 0.1954668 0.4235714 0.0000000 0.4479540 0.5520460 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 13.95078 46.34349</span> +<span class="r-out co"><span class="r-pr">#></span> A1 49.75347 165.27745</span> +<span class="r-out co"><span class="r-pr">#></span> B1 37.26905 123.80511</span> +<span class="r-out co"><span class="r-pr">#></span> C1 11.23129 37.30955</span> +<span class="r-out co"><span class="r-pr">#></span> A2 28.50690 94.69789</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span> <span class="co"># Compare with the results obtained in the original publication</span></span></span> +<span class="r-in"><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">schaefer07_complex_results</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> compound parameter KinGUI ModelMaker deviation</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent degradation rate 0.0496 0.0506 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 parent DT50 13.9900 13.6900 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9</span> +<span class="r-out co"><span class="r-pr">#></span> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 5 metabolite A1 DT50 49.9600 50.8900 1.8</span> +<span class="r-out co"><span class="r-pr">#></span> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6</span> +<span class="r-out co"><span class="r-pr">#></span> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7</span> +<span class="r-out co"><span class="r-pr">#></span> 8 metabolite B1 DT50 39.6100 40.2400 1.6</span> +<span class="r-out co"><span class="r-pr">#></span> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9</span> +<span class="r-out co"><span class="r-pr">#></span> 11 metabolite C1 DT50 10.8700 9.9000 9.8</span> +<span class="r-out co"><span class="r-pr">#></span> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4</span> +<span class="r-out co"><span class="r-pr">#></span> 14 metabolite A2 DT50 28.2400 28.4500 0.7</span> +</code></pre></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 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