aboutsummaryrefslogblamecommitdiff
path: root/docs/reference/CAKE_export.html
blob: d36f5ed94b42ad212e9432b01fd0c867e3590f1d (plain) (tree)
1
2
3
4
5
6
7
8
9
               

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  

                                                                               

                                                              
 
                                                    
                                                                                    









                                                                                                                               
                                                                                                                                     



                                                      
                                     







                                                                                                 
                                            








                                                                                                 


                                                                                                                                                      







                                                                                                                             


                                                                                                                


                                                                               
            


                                       

                                                                  
                                             


      
                                       



                           
 
                                

                                 
                                                                  
                                                                                                                                                                       



                                                              

                                                                                

          
















                                                                                                                                                                                                                                               
 









                                                                        
                                                                       
























                                                                   
                                                      


                     
                         
          

        
                                                                 

                                                                                      

      
 

                                            


                     
                                                                                                             
      
 
                     


  
 
  
 
                
 
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Export a list of datasets format to a CAKE study file — CAKE_export • 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="Export a list of datasets format to a CAKE study file — CAKE_export"><meta property="og:description" content="In addition to the datasets, the pathways in the degradation model can be
specified as well."><!-- 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">1.1.0</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/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</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>
    <li>
      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
    </li>
  </ul></li>
<li>
  <a href="../news/index.html">News</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/jranke/mkin/" class="external-link">
    <span class="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>Export a list of datasets format to a CAKE study file</h1>
    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/CAKE_export.R" class="external-link"><code>R/CAKE_export.R</code></a></small>
    <div class="hidden name"><code>CAKE_export.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>In addition to the datasets, the pathways in the degradation model can be
specified as well.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">CAKE_export</span><span class="op">(</span>
  <span class="va">ds</span>,
  map <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>parent <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,
  links <span class="op">=</span> <span class="cn">NA</span>,
  filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>,
  path <span class="op">=</span> <span class="st">"."</span>,
  overwrite <span class="op">=</span> <span class="cn">FALSE</span>,
  study <span class="op">=</span> <span class="st">"Codlemone aerobic soil degradation"</span>,
  description <span class="op">=</span> <span class="st">""</span>,
  time_unit <span class="op">=</span> <span class="st">"days"</span>,
  res_unit <span class="op">=</span> <span class="st">"% AR"</span>,
  comment <span class="op">=</span> <span class="st">"Created using mkin::CAKE_export"</span>,
  date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>,
  optimiser <span class="op">=</span> <span class="st">"IRLS"</span>
<span class="op">)</span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>ds</dt>
<dd><p>A named list of datasets in long format as compatible with
<code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
<dt>map</dt>
<dd><p>A character vector with CAKE compartment names (Parent, A1, ...),
named with the names used in the list of datasets.</p></dd>
<dt>links</dt>
<dd><p>An optional character vector of target compartments, named with
the names of the source compartments. In order to make this easier, the
names are used as in the datasets supplied.</p></dd>
<dt>filename</dt>
<dd><p>Where to write the result. Should end in .csf in order to be
compatible with CAKE.</p></dd>
<dt>path</dt>
<dd><p>An optional path to the output file.</p></dd>
<dt>overwrite</dt>
<dd><p>If TRUE, existing files are overwritten.</p></dd>
<dt>study</dt>
<dd><p>The name of the study.</p></dd>
<dt>description</dt>
<dd><p>An optional description.</p></dd>
<dt>time_unit</dt>
<dd><p>The time unit for the residue data.</p></dd>
<dt>res_unit</dt>
<dd><p>The unit used for the residues.</p></dd>
<dt>comment</dt>
<dd><p>An optional comment.</p></dd>
<dt>date</dt>
<dd><p>The date of file creation.</p></dd>
<dt>optimiser</dt>
<dd><p>Can be OLS or IRLS.</p></dd>
</dl></div>
    <div id="value">
    <h2>Value</h2>
    <p>The function is called for its side effect.</p>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Johannes Ranke</p>
    </div>

  </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></p><p>Developed by Johannes Ranke.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>

      </footer></div>

  


  

  </body></html>

Contact - Imprint