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diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html new file mode 100644 index 00000000..8d162cd8 --- /dev/null +++ b/inst/web/mkinmod.html @@ -0,0 +1,247 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>mkinmod. 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"> +<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="#">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 model with one or more state variables +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><div>mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)</div></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.inside-r.org/packages/cran/inline/docs/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'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...) +SFO <- mkinmod(parent = list(type = "SFO")) + +# One parent compound, one metabolite, both single first order +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) +</div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'> +# The above model used to be specified like this, before the advent of mkinsub() +SFO_SFO <- mkinmod( + parent = list(type = "SFO", to = "m1"), + m1 = list(type = "SFO")) +</div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'> +# Show details of creating the C function +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), verbose = TRUE) +</div> +<div class='output'>Compilation argument: + /usr/lib/R/bin/R CMD SHLIB file5a355b71ca9.c 2> file5a355b71ca9.c.err.txt +Program source: + 1: #include <R.h> + 2: + 3: + 4: static double parms [3]; + 5: #define k_parent_sink parms[0] + 6: #define k_parent_m1 parms[1] + 7: #define k_m1_sink parms[2] + 8: + 9: void initpar(void (* odeparms)(int *, double *)) { + 10: int N = 3; + 11: odeparms(&N, parms); + 12: } + 13: + 14: + 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { + 16: + 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; + 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; + 19: } +</div> +<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong> +<div class='input'> +# If we have several parallel metabolites +# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) +m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), + M1 = mkinsub("SFO"), + M2 = mkinsub("SFO"), + use_of_ff = "max", quiet = TRUE) + +## Not run: +# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, +# synthetic_data_for_UBA_2014[[12]]$data, +# quiet = TRUE) +# ## End(Not run) +</div></pre> + </div> + <div class="span4"> + <!-- <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>. 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