aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/test_data_from_UBA_2014.html
blob: 6059a4d29505a7a86446d3d97c51e959d9fc587a (plain) (tree)
1
2
3
4
5
6
7
8
9
10

                                                  
                






                                                                                                                            
 
               
                                                                                                                                                                                 

                  
                                                                                                                                                                                                             
 




                                                                                                                                                                                                  

                           

                                                                                                                                                                                                        
 
                     
                                                                                                                                                                                          
 
                    

                                                                                                                                                                                             
 

                                             
                                     


 
 
                                                                                                                                           

                                                                                                                            


 
 
                

                                                                                                                                                                                                    






                                                                               
 

         
                                             




                                                                            

                                                                                                                               



                                      

                                                            
                                                                                                                                        
             
          
 





















                                                                                                 
                                                                                                   

         
                                                                                                                             



                                                                                                      


                                                                                                                





                                       
                                              





                                                    
           
      




                                
 

               
                 


                                                                                     

                                                                          

          
                                 

                                                                                          
          

                                                                            

 


                                                                                                                
                                                                   

                                                                                                                                                


     



                                                                                      

                                                                                            

                                                                                                          





                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            









                                                                                                                                                                                                                                                                                                                                                                                             

                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                


                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             








                                                                                 

                                                                                 
                                
                                


                                

                                

                                
                                                                                                                                                                                                                            

                                    
                                    
                                    
                                                                  
            
        



                                                                 


        
 





                                     
                                                                                
      
 


               

  
 

         
 
 
<!-- 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/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
<!-- Bootstrap -->

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />

<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>

<!-- bootstrap-toc -->
<link rel="stylesheet" href="../bootstrap-toc.css">
<script src="../bootstrap-toc.js"></script>

<!-- Font Awesome icons -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>

<!-- headroom.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>




<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" />
<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation
 software packages (Ranke, 2014)." />




<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>

<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->



  </head>

  <body data-spy="scroll" data-target="#toc">
    <div class="container template-reference-topic">
      <header>
      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle 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">0.9.50.2</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">
        <li>
  <a href="http://github.com/jranke/mkin/">
    <span class="fab fa fab fa-github fa-lg"></span>
     
  </a>
</li>
      </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'>
    <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>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top">
      <h2 data-toc-skip>Contents</h2>
    </nav>
  </div>
</div>


      <footer>
      <div class="copyright">
  <p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
</div>

      </footer>
   </div>

  


  </body>
</html>


Contact - Imprint