<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
<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>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
<!-- mathjax -->
<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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>
<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">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="../index.html">mkin</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../reference/index.html">Reference</a>
</li>
<li>
<a href="../articles/index.html">Articles</a>
</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="fa 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>Function to set up a kinetic model with one or more state variables</h1>
</div>
<p>The function usually takes several expressions, each assigning a compound name to
a list, specifying the kinetic model type and reaction or transfer to other
observed compartments. Instead of specifying several expressions, a list
of lists can be given in the speclist argument.</p>
<p>For the definition of model types and their parameters, the equations given
in the FOCUS and NAFTA guidance documents are used.</p>
<pre><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
<dl class="dl-horizontal">
<dt>...</dt>
<dd>
For each observed variable, a list has to be specified as an argument, containing
at least a component <code>type</code>, specifying the type of kinetics to use
for the variable. Currently, single first order kinetics "SFO",
indeterminate order rate equation kinetics "IORE", or
single first order with reversible binding "SFORB" are implemented for all
variables, while
"FOMC", "DFOP" and "HS" can additionally be chosen for the first
variable which is assumed to be the source compartment.
Additionally, each component of the list can include a character vector <code>to</code>,
specifying names of variables to which a transfer is to be assumed in the
model.
If the argument <code>use_of_ff</code> is set to "min" (default) and the model for
the compartment is "SFO" or "SFORB", an additional component of the list
can be "sink=FALSE" effectively fixing the flux to sink to zero.
</dd>
<dt>use_of_ff</dt>
<dd>
Specification of the use of formation fractions in the model equations and, if
applicable, the coefficient matrix. If "min", a minimum use of formation
fractions is made in order to avoid fitting the product of formation fractions
and rate constants. If "max", formation fractions are always used.
</dd>
<dt>speclist</dt>
<dd>
The specification of the observed variables and their submodel types and
pathways can be given as a single list using this argument. Default is NULL.
</dd>
<dt>quiet</dt>
<dd>
Should messages be suppressed?
</dd>
<dt>verbose</dt>
<dd>
If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give
detailed information about the C function being built.
</dd>
</dl>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>The IORE submodel is not well tested (yet). When using this model for metabolites,
you may want to read the second note in the help page to
<code><a href='mkinfit.html'>mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>FOCUS (2006) “Guidance Document on Estimating Persistence and
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration” Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental
Media</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
<span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))
<span class='co'># One parent compound, one metabolite, both single first order</span>
<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'>## Not run: ------------------------------------</span>
<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span>
<span class='co'># SFO_SFO <- mkinmod(</span>
<span class='co'># parent = list(type = "SFO", to = "m1"),</span>
<span class='co'># m1 = list(type = "SFO"))</span>
<span class='co'># </span>
<span class='co'># # Show details of creating the C function</span>
<span class='co'># SFO_SFO <- mkinmod(</span>
<span class='co'># parent = mkinsub("SFO", "m1"),</span>
<span class='co'># m1 = mkinsub("SFO"), verbose = TRUE)</span>
<span class='co'># </span>
<span class='co'># # If we have several parallel metabolites </span>
<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='co'># m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span>
<span class='co'># M1 = mkinsub("SFO"),</span>
<span class='co'># M2 = mkinsub("SFO"),</span>
<span class='co'># use_of_ff = "max", quiet = TRUE)</span>
<span class='co'># </span>
<span class='co'># fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, </span>
<span class='co'># synthetic_data_for_UBA_2014[[12]]$data,</span>
<span class='co'># quiet = TRUE)</span>
<span class='co'>## ---------------------------------------------</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#note">Note</a></li>
<li><a href="#references">References</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
<h2>Author</h2>
Johannes Ranke
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>