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authorJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-03-02 18:03:54 +0100
commit2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch)
treef286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/schaefer07_complex_case.html
parent351248d07f810ccb6c497633a02cd48ee35526e6 (diff)
Make tests more platform independent, update docs
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<h1>Metabolism data set used for checking the software quality of KinGUI</h1>
@@ -151,93 +90,109 @@
The results from the fitting are also included.</p>
</div>
- <pre class="usage"><span class='va'>schaefer07_complex_case</span></pre>
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="va">schaefer07_complex_case</span></code></pre></div>
+ </div>
+
+ <div id="format">
+ <h2>Format</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>
- <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+ <dt><code>C1</code></dt>
+<dd><p>a numeric vector</p></dd>
+
+ <dt><code>A2</code></dt>
+<dd><p>a numeric vector</p></dd>
- <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>
- <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
-
+ </div>
+ <div id="references">
+ <h2>References</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>
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='va'>data</span> <span class='op'>&lt;-</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 class='va'>model</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>
- parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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'>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>,
- A1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>,
- B1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
- C1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>,
- A2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>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>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span>
- <span class='va'>fit</span> <span class='op'>&lt;-</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 class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; $ff
-#&gt; parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink
-#&gt; 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; parent 13.95078 46.34350
-#&gt; A1 49.75342 165.27728
-#&gt; B1 37.26908 123.80520
-#&gt; C1 11.23131 37.30961
-#&gt; A2 28.50624 94.69567
-#&gt; </div><div class='input'> <span class='co'># }</span>
- <span class='co'># Compare with the results obtained in the original publication</span>
- <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; compound parameter KinGUI ModelMaker deviation
-#&gt; 1 parent degradation rate 0.0496 0.0506 2.0
-#&gt; 2 parent DT50 13.9900 13.6900 2.2
-#&gt; 3 metabolite A1 formation fraction 0.3803 0.3696 2.9
-#&gt; 4 metabolite A1 degradation rate 0.0139 0.0136 2.2
-#&gt; 5 metabolite A1 DT50 49.9600 50.8900 1.8
-#&gt; 6 metabolite B1 formation fraction 0.1866 0.1818 2.6
-#&gt; 7 metabolite B1 degradation rate 0.0175 0.0172 1.7
-#&gt; 8 metabolite B1 DT50 39.6100 40.2400 1.6
-#&gt; 9 metabolite C1 formation fraction 0.4331 0.4486 3.5
-#&gt; 10 metabolite C1 degradation rate 0.0638 0.0700 8.9
-#&gt; 11 metabolite C1 DT50 10.8700 9.9000 9.8
-#&gt; 12 metabolite A2 formation fraction 0.4529 0.4559 0.7
-#&gt; 13 metabolite A2 degradation rate 0.0245 0.0244 0.4
-#&gt; 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre>
+ <div id="ref-examples">
+ <h2>Examples</h2>
+ <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">data</span> <span class="op">&lt;-</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 class="r-in"><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span>
+<span class="r-in"> 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 class="r-in"> 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 class="r-in"> 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 class="r-in"> 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 class="r-in"> 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 class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"> <span class="co"># \dontrun{</span></span>
+<span class="r-in"> <span class="va">fit</span> <span class="op">&lt;-</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 class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</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 class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DT50 DT90</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 13.95078 46.34350</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> A1 49.75342 165.27728</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> B1 37.26908 123.80520</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> C1 11.23131 37.30961</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> A2 28.50624 94.69567</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-in"> <span class="co"># }</span></span>
+<span class="r-in"> <span class="co"># Compare with the results obtained in the original publication</span></span>
+<span class="r-in"> <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 class="r-out co"><span class="r-pr">#&gt;</span> compound parameter KinGUI ModelMaker deviation</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 parent degradation rate 0.0496 0.0506 2.0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2 parent DT50 13.9900 13.6900 2.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5 metabolite A1 DT50 49.9600 50.8900 1.8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8 metabolite B1 DT50 39.6100 40.2400 1.6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 11 metabolite C1 DT50 10.8700 9.9000 9.8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 14 metabolite A2 DT50 28.2400 28.4500 0.7</span>
+</code></pre></div>
+ </div>
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