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authorJohannes Ranke <jranke@uni-bremen.de>2022-08-10 16:04:48 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2022-08-10 16:04:48 +0200
commitfcef764f3688b01a4c6e92915ed68c5e54bc165f (patch)
tree7d5f0b43485d2e99e1e0ea999d0ce47b6914839d /docs/dev/reference/CAKE_export.html
parentbc8ce24677e953e003f7904564b7767537e01ca2 (diff)
parent6178249bbb5e9de7cb7f34287ee7de28a68fed6c (diff)
Merge branch 'v1.1.2'
Diffstat (limited to 'docs/dev/reference/CAKE_export.html')
-rw-r--r--docs/dev/reference/CAKE_export.html282
1 files changed, 110 insertions, 172 deletions
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
index e187772f..47efd056 100644
--- a/docs/dev/reference/CAKE_export.html
+++ b/docs/dev/reference/CAKE_export.html
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+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]>
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-<![endif]-->
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+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+
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-
- <body data-spy="scroll" data-target="#toc">
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+ <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">
@@ -73,23 +18,21 @@ specified as well." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span>
</span>
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- <ul class="nav navbar-nav">
- <li>
+ <ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Functions and data</a>
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+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
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+ <ul class="dropdown-menu" role="menu"><li>
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<li>
@@ -99,6 +42,9 @@ specified as well." />
<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>
@@ -113,34 +59,27 @@ specified as well." />
<li>
<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
</li>
- </ul>
-</li>
+ </ul></li>
<li>
<a href="../news/index.html">News</a>
</li>
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+ </ul><ul class="nav navbar-nav navbar-right"><li>
+ <a href="https://github.com/jranke/mkin/" class="external-link">
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+ </ul></div><!--/.nav-collapse -->
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+ </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>
+ <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>
@@ -149,116 +88,115 @@ specified as well." />
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
+ <div id="ref-usage">
+ <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">CAKE_export</span><span class="op">(</span></span>
+<span> <span class="va">ds</span>,</span>
+<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>,</span>
+<span> links <span class="op">=</span> <span class="cn">NA</span>,</span>
+<span> filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>,</span>
+<span> path <span class="op">=</span> <span class="st">"."</span>,</span>
+<span> overwrite <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span> study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>,</span>
+<span> description <span class="op">=</span> <span class="st">""</span>,</span>
+<span> time_unit <span class="op">=</span> <span class="st">"days"</span>,</span>
+<span> res_unit <span class="op">=</span> <span class="st">"% AR"</span>,</span>
+<span> comment <span class="op">=</span> <span class="st">""</span>,</span>
+<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>,</span>
+<span> optimiser <span class="op">=</span> <span class="st">"IRLS"</span></span>
+<span><span class="op">)</span></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></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>
+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>
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- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
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+ <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
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