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diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html new file mode 100644 index 00000000..9dd8fca0 --- /dev/null +++ b/docs/reference/mkinmod.html @@ -0,0 +1,206 @@ +<!-- 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>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/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" 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="../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"> + <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="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://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="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <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>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> + + <div class="Value"> + <h2>Value</h2> + + <p>A list of class <code>mkinmod</code> for use with <code>mkinfit</code>, containing</p> + </div> + + <div class="Note"> + <h2>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>mkinfit</code>.</p> + </div> + + <div class="References"> + <h2>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> + </div> + + <h2 id="examples">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'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></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"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> |