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diff --git a/docs/mkinmod.html b/docs/mkinmod.html deleted file mode 100644 index afbb9cc2..00000000 --- a/docs/mkinmod.html +++ /dev/null @@ -1,221 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>mkinmod. 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 model with one or more state variables -</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="symbol">...</span><span class="keyword">,</span> <span class="argument">use_of_ff</span> <span class="argument">=</span> <span class="string">"min"</span><span class="keyword">,</span> <span class="argument">speclist</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">verbose</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <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><a href='http://www.rdocumentation.org/packages/inline/topics/cfunction'>cfunction</a></code> if applicable to give - detailed information about the C function being built. - </dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <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> - - </div> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> - A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing - <dt>diffs</dt><dd> A vector of string representations of differential equations, - one for each modelling variable. </dd></p> - - <p><dt>parms</dt><dd> A vector of parameter names occurring in the differential equations. </dd></p> - - <p><dt>map</dt><dd> A list containing named character vectors for each observed variable, specifying - the modelling variables by which it is represented. </dd></p> - - <p><dt>use_of_ff</dt><dd> The content of <code>use_of_ff</code> is passed on in this list component. </dd></p> - - <p><dt>coefmat</dt><dd> The coefficient matrix, if the system of differential equations can be - represented by one. </dd></p> - - <p></dl></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><a href='mkinfit.html'>mkinfit</a></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="comment"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> -<span class="symbol">SFO</span> <span class="assignement"><-</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="keyword">)</span> - -<span class="comment"># One parent compound, one metabolite, both single first order</span> -<span class="symbol">SFO_SFO</span> <span class="assignement"><-</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">## Not run: ------------------------------------</span> -<span class="comment"># # The above model used to be specified like this, before the advent of mkinsub()</span> -<span class="comment"># SFO_SFO <- mkinmod(</span> -<span class="comment"># parent = list(type = "SFO", to = "m1"),</span> -<span class="comment"># m1 = list(type = "SFO"))</span> -<span class="comment"># </span> -<span class="comment"># # Show details of creating the C function</span> -<span class="comment"># SFO_SFO <- mkinmod(</span> -<span class="comment"># parent = mkinsub("SFO", "m1"),</span> -<span class="comment"># m1 = mkinsub("SFO"), verbose = TRUE)</span> -<span class="comment"># </span> -<span class="comment"># # If we have several parallel metabolites </span> -<span class="comment"># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> -<span class="comment"># m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span> -<span class="comment"># M1 = mkinsub("SFO"),</span> -<span class="comment"># M2 = mkinsub("SFO"),</span> -<span class="comment"># use_of_ff = "max", quiet = TRUE)</span> -<span class="comment"># </span> -<span class="comment"># fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, </span> -<span class="comment"># synthetic_data_for_UBA_2014[[12]]$data,</span> -<span class="comment"># quiet = TRUE)</span> -<span class="comment">## ---------------------------------------------</span></div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>mkinmod</li> - </ul> - <ul> - <li> models </li> - </ul> --> - - - - <h2>Author</h2> - - Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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