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authorJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:05:15 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:05:15 +0100
commit3151647526f299686b68420a83ae38cd7f3d08f5 (patch)
treec061b5a23ac6cc5644c6851012105b185715ef5e /inst/web/mkinsub.html
parent415ca2bea5d5c3815bd9f8fa1566cec5bb3fc775 (diff)
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+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+<title>mkinsub. mkin 0.9-41</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+<meta name="author" content="
+ Johannes Ranke
+">
+
+<link href="css/bootstrap.css" rel="stylesheet">
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+ }
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+</script>
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+ </head>
+
+ <body>
+ <div class="navbar">
+ <div class="navbar-inner">
+ <div class="container">
+ <a class="brand" href="#">mkin 0.9-41</a>
+ <div class="nav">
+ <ul class="nav">
+ <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+</div>
+
+ <div class="container">
+ <header>
+
+ </header>
+
+ <h1>
+ Function to set up a kinetic submodel for one state variable
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><div>mkinsub(submodel, to&nbsp;=&nbsp;NULL, sink&nbsp;=&nbsp;TRUE, full_name&nbsp;=&nbsp;NA)</div></pre>
+
+ <h2>Arguments</h2>
+ <dl>
+ <dt>submodel</dt>
+ <dd>
+ Character vector of length one to specify the submodel type. See
+ <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.
+ </dd>
+ <dt>to</dt>
+ <dd>
+ Vector of the names of the state variable to which a transformation
+ shall be included in the model.
+ </dd>
+ <dt>sink</dt>
+ <dd>
+ Should a pathway to sink be included in the model in addition to the
+ pathways to other state variables?
+ </dd>
+ <dt>full_name</dt>
+ <dd>
+ An optional name to be used e.g. for plotting fits performed with the model.
+ You can use non-ASCII characters here, but then your R code will not be
+ portable, <em>i.e.</em> may produce unintended plot results on other
+ operating systems or system configurations.
+ </dd>
+ </dl>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <p>This is a convenience function to set up the lists used as arguments for
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</p>
+
+ </div>
+
+ <div class="Value">
+ <h2>Value</h2>
+
+ <p><dl>
+ A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.
+</dl></p>
+
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'># One parent compound, one metabolite, both single first order.
+SFO_SFO &lt;- mkinmod(
+ parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;),
+ m1 = list(type = &quot;SFO&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+# The same model using mkinsub
+SFO_SFO.2 &lt;- mkinmod(
+ parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
+ m1 = mkinsub(&quot;SFO&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+# Now supplying full names
+SFO_SFO.2 &lt;- mkinmod(
+ parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;, full_name = &quot;Test compound&quot;),
+ m1 = mkinsub(&quot;SFO&quot;, full_name = &quot;Metabolite M1&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong></pre>
+ </div>
+ <div class="span4">
+ <!-- <ul>
+ <li>mkinsub</li>
+ </ul>
+ <ul>
+
+ </ul> -->
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
+
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