Create up to date pkgdown docs in development mode

author: Johannes Ranke <jranke@uni-bremen.de> 2020-05-27 06:06:08 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-05-27 06:06:08 +0200
commit: a77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
tree: e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/CAKE_export.html
parent: 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
1 files changed, 261 insertions, 0 deletions
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
new file mode 100644
index 00000000..ce8a3444
--- /dev/null
+++ b/docs/dev/reference/CAKE_export.html
@@ -0,0 +1,261 @@
+<!-- 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." />
+
+
+<meta name="robots" content="noindex">
+
+<!-- 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-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</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="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>Export a list of datasets format to a CAKE study file</h1>
+    <small class="dont-index">Source: <a href='http://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='no'>ds</span>,
+  <span class='kw'>map</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>),
+  <span class='kw'>links</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>filename</span> <span class='kw'>=</span> <span class='st'>"CAKE_export.csf"</span>,
+  <span class='kw'>path</span> <span class='kw'>=</span> <span class='st'>"."</span>,
+  <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>study</span> <span class='kw'>=</span> <span class='st'>"Codlemone aerobic soil degradation"</span>,
+  <span class='kw'>description</span> <span class='kw'>=</span> <span class='st'>""</span>,
+  <span class='kw'>time_unit</span> <span class='kw'>=</span> <span class='st'>"days"</span>,
+  <span class='kw'>res_unit</span> <span class='kw'>=</span> <span class='st'>"% AR"</span>,
+  <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>"Created using mkin::CAKE_export"</span>,
+  <span class='kw'>date</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.Date</a></span>(),
+  <span class='kw'>optimiser</span> <span class='kw'>=</span> <span class='st'>"IRLS"</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>
+
+  </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>
+
+
author	Johannes Ranke <jranke@uni-bremen.de>	2020-05-27 06:06:08 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-05-27 06:06:08 +0200
commit	a77a10ea6c607346778ba0700b3b66ac393101a2 (patch)
tree	e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/CAKE_export.html
parent	675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)