path: root/docs/reference/CAKE_export.html



<!-- 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>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">1.0.3</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>
    <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/">
    <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/master/R/CAKE_export.R'><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>

    <pre class="usage"><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'>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'>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></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>ds</th>
      <td><p>A named list of datasets in long format as compatible with
<code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
    </tr>
    <tr>
      <th>map</th>
      <td><p>A character vector with CAKE compartment names (Parent, A1, ...),
named with the names used in the list of datasets.</p></td>
    </tr>
    <tr>
      <th>links</th>
      <td><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></td>
    </tr>
    <tr>
      <th>filename</th>
      <td><p>Where to write the result. Should end in .csf in order to be
compatible with CAKE.</p></td>
    </tr>
    <tr>
      <th>path</th>
      <td><p>An optional path to the output file.</p></td>
    </tr>
    <tr>
      <th>overwrite</th>
      <td><p>If TRUE, existing files are overwritten.</p></td>
    </tr>
    <tr>
      <th>study</th>
      <td><p>The name of the study.</p></td>
    </tr>
    <tr>
      <th>description</th>
      <td><p>An optional description.</p></td>
    </tr>
    <tr>
      <th>time_unit</th>
      <td><p>The time unit for the residue data.</p></td>
    </tr>
    <tr>
      <th>res_unit</th>
      <td><p>The unit used for the residues.</p></td>
    </tr>
    <tr>
      <th>comment</th>
      <td><p>An optional comment.</p></td>
    </tr>
    <tr>
      <th>date</th>
      <td><p>The date of file creation.</p></td>
    </tr>
    <tr>
      <th>optimiser</th>
      <td><p>Can be OLS or IRLS.</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>The function is called for its side effect.</p>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

    <p>Johannes Ranke</p>

  </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> 1.6.1.</p>
</div>

      </footer>
   </div>

  
  </body>
</html>