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<title>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin</title>


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<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" />
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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 class='dl-horizontal'>
    <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;                         Estimate se_notrans      t value       Pr(&gt;t)
#&gt; parent_w_0          9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
#&gt; k_parent_w_sink     3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
#&gt; k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
#&gt; k_parent_s_sink     5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
#&gt; k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
#&gt; sigma               2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
#&gt;                           Lower       Upper
#&gt; parent_w_0          91.48420503 100.4871438
#&gt; k_parent_w_sink      0.30668904   0.4234571
#&gt; k_parent_w_parent_s  0.03423904   0.1062455
#&gt; k_parent_s_sink      0.00000000         Inf
#&gt; k_parent_s_parent_w  0.02289956   0.2404043
#&gt; sigma                2.00184022   3.9639169</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 0.09246946       5  6
#&gt; parent_w 0.06377096       3  3
#&gt; parent_s 0.20882325       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 0.859186619 89.1008474 1.113866e-26 74.755959756
#&gt; k_parent        0.12081956 0.004601922 26.2541544 1.077373e-16  0.111561582
#&gt; k_M1            0.84258649 0.806231419  1.0450926 1.545475e-01  0.113839803
#&gt; k_M2            0.04210878 0.017083049  2.4649453 1.170195e-02  0.018013807
#&gt; k_M3            0.01122919 0.007245890  1.5497322 6.885127e-02  0.002909463
#&gt; f_parent_to_M1  0.32240199 0.240803555  1.3388589 9.820820e-02           NA
#&gt; f_parent_to_M2  0.16099854 0.033691991  4.7785403 6.531224e-05           NA
#&gt; f_M1_to_M3      0.27921501 0.269443514  1.0362655 1.565440e-01  0.022992937
#&gt; f_M2_to_M3      0.55641331 0.595125445  0.9349513 1.807725e-01  0.008003317
#&gt; sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
#&gt;                      Upper
#&gt; parent_0       78.35255192
#&gt; k_parent        0.13084582
#&gt; k_M1            6.23641265
#&gt; k_M2            0.09843279
#&gt; k_M3            0.04333950
#&gt; f_parent_to_M1          NA
#&gt; f_parent_to_M2          NA
#&gt; f_M1_to_M3      0.86443083
#&gt; f_M2_to_M3      0.99489847
#&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       0.26551209       2  5
#&gt; M2       0.20327575       2  5
#&gt; M3       0.05196549       3  4</div><div class='input'>  # }
</div></pre>
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