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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
commita77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
treee91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/test_data_from_UBA_2014.html
parent675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
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+ <h1>Three experimental datasets from two water sediment systems and one soil</h1>
+
+ <div class="hidden name"><code>test_data_from_UBA_2014.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>The datasets were used for the comparative validation of several kinetic evaluation
+ software packages (Ranke, 2014).</p>
+ </div>
+
+ <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre>
+
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>.
+ Each dataset has, among others, the following components</p><dl'>
+ <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd>
+ <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
+
+</dl>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+ zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span>
+ <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span>
+ <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span>
+ <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span>
+ <span class='co'># generally considered deprecated due to the frequent occurrence of such</span>
+ <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span>
+ <span class='co'># model).</span>
+ <span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
+ <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
+ <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower Upper
+#&gt; parent_w_0 95.91998116 NA NA NA NA NA
+#&gt; k_parent_w 0.41145375 NA NA NA NA NA
+#&gt; k_parent_s 0.04663944 NA NA NA NA NA
+#&gt; f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA
+#&gt; f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA
+#&gt; sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.1090929 5 6
+#&gt; parent_w 0.0817436 3 3
+#&gt; parent_s 0.1619965 2 3</div><div class='input'>
+ <span class='co'># This is the evaluation used for the validation of software packages</span>
+ <span class='co'># in the expertise from 2014</span>
+ <span class='no'>m_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
+ <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
+ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>),
+ <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
+ <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; Estimate se_notrans t value Pr(&gt;t) Lower
+#&gt; parent_0 76.55425584 0.859186419 89.1008681 1.113862e-26 74.755958720
+#&gt; k_parent 0.12081956 0.004601919 26.2541703 1.077361e-16 0.111561576
+#&gt; k_M1 0.84258629 0.806165149 1.0451783 1.545282e-01 0.113778910
+#&gt; k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013823
+#&gt; k_M3 0.01122919 0.007245870 1.5497364 6.885076e-02 0.002909418
+#&gt; f_parent_to_M1 0.32240193 0.240785518 1.3389590 9.819221e-02 NA
+#&gt; f_parent_to_M2 0.16099854 0.033691991 4.7785404 6.531224e-05 NA
+#&gt; f_M1_to_M3 0.27921506 0.269425582 1.0363346 1.565282e-01 0.022977955
+#&gt; f_M2_to_M3 0.55641331 0.595121774 0.9349571 1.807710e-01 0.008002320
+#&gt; sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778
+#&gt; Upper
+#&gt; parent_0 78.35255297
+#&gt; k_parent 0.13084582
+#&gt; k_M1 6.23974738
+#&gt; k_M2 0.09843271
+#&gt; k_M3 0.04334017
+#&gt; f_parent_to_M1 NA
+#&gt; f_parent_to_M2 NA
+#&gt; f_M1_to_M3 0.86450905
+#&gt; f_M2_to_M3 0.99489911
+#&gt; sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt; err.min n.optim df
+#&gt; All data 0.09649963 9 20
+#&gt; parent 0.04721283 2 6
+#&gt; M1 0.26551208 2 5
+#&gt; M2 0.20327575 2 5
+#&gt; M3 0.05196550 3 4</div><div class='input'> # }
+</div></pre>
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