<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin</title> <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons 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navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.5</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> </li> <li> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> </ul> </li> <li> <a href="../news/index.html">News</a> </li> </ul> <ul class="nav navbar-nav navbar-right"> </ul> </div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> </header> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <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'> </div><div class='input'> <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'><-</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'>#> <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'><-</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>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) #> parent_w_0 9.598567e+01 2.12351789 4.520126e+01 9.476190e-18 #> k_parent_w_sink 3.603743e-01 0.03149282 1.144306e+01 4.126593e-09 #> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04 #> k_parent_s_sink 5.108964e-11 0.09482736 5.387647e-10 5.000000e-01 #> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01 #> sigma 2.982879e+00 0.50545649 5.901356e+00 1.454535e-05 #> Lower Upper #> parent_w_0 91.48420503 100.4871438 #> k_parent_w_sink 0.30668904 0.4234571 #> k_parent_w_parent_s 0.03423904 0.1062455 #> k_parent_s_sink 0.00000000 Inf #> k_parent_s_parent_w 0.02289956 0.2404043 #> 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'>#> err.min n.optim df #> All data 0.09246946 5 6 #> parent_w 0.06377096 3 3 #> 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'><-</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://www.rdocumentation.org/packages/base/topics/c'>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'>#> <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'><-</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>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_0 76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756 #> k_parent 0.12081956 0.004601922 26.2541544 1.077373e-16 0.111561582 #> k_M1 0.84258649 0.806231419 1.0450926 1.545475e-01 0.113839803 #> k_M2 0.04210878 0.017083049 2.4649453 1.170195e-02 0.018013807 #> k_M3 0.01122919 0.007245890 1.5497322 6.885127e-02 0.002909463 #> f_parent_to_M1 0.32240199 0.240803555 1.3388589 9.820820e-02 NA #> f_parent_to_M2 0.16099854 0.033691991 4.7785403 6.531224e-05 NA #> f_M1_to_M3 0.27921501 0.269443514 1.0362655 1.565440e-01 0.022992937 #> f_M2_to_M3 0.55641331 0.595125445 0.9349513 1.807725e-01 0.008003317 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper #> parent_0 78.35255192 #> k_parent 0.13084582 #> k_M1 6.23641265 #> k_M2 0.09843279 #> k_M3 0.04333950 #> f_parent_to_M1 NA #> f_parent_to_M2 NA #> f_M1_to_M3 0.86443083 #> f_M2_to_M3 0.99489847 #> 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'>#> err.min n.optim df #> All data 0.09649963 9 20 #> parent 0.04721283 2 6 #> M1 0.26551209 2 5 #> M2 0.20327575 2 5 #> M3 0.05196549 3 4</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#format">Format</a></li> <li><a href="#source">Source</a></li> <li><a href="#examples">Examples</a></li> </ul> </div> </div> <footer> <div 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