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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
commit7c62da1269e8910a210ba1917d4dc62d186d5606 (patch)
tree57da1e788f84fe95352ff66d22a9da56dc86f9c3 /docs/mkinsub.html
parent38f9e15f0c972c1516ae737a2bca8d7789581bbd (diff)
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-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>mkinsub. mkin 0.9.44.9000</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">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</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="index.html">mkin 0.9.44.9000</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</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><span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="symbol">submodel</span><span class="keyword">,</span> <span class="argument">to</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">sink</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">,</span> <span class="argument">full_name</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">NA</span><span class="keyword">)</span></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'><span class="comment"># One parent compound, one metabolite, both single first order.</span>
-<span class="symbol">SFO_SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span>
- <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">to</span> <span class="argument">=</span> <span class="string">"m1"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>
-<span class="comment"># The same model using mkinsub</span>
-<span class="symbol">SFO_SFO.2</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span>
- <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>
-<span class="comment"># Now supplying full names</span>
-<span class="symbol">SFO_SFO.2</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span>
- <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">,</span> <span class="argument">full_name</span> <span class="argument">=</span> <span class="string">"Test compound"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">full_name</span> <span class="argument">=</span> <span class="string">"Metabolite M1"</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>mkinsub</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
- Johannes Ranke
-
-
- </div>
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