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diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 1343abcc..de9815d4 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title> - — mkinmod • mkin</title> +<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> @@ -26,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/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> @@ -71,6 +72,9 @@ <li> <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> + <li> + <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> </ul> </li> <li> @@ -96,8 +100,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1> -</h1> + <h1>Function to set up a kinetic model with one or more state variables</h1> </div> @@ -105,58 +108,67 @@ 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 +<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> + <pre class="usage"><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 + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>...</th> + <td><p>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 + 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 + "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 + 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.</p></td> + </tr> + <tr> + <th>use_of_ff</th> + <td><p>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> + and rate constants. If "max", formation fractions are always used.</p></td> + </tr> + <tr> + <th>speclist</th> + <td><p>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.</p></td> + </tr> + <tr> + <th>quiet</th> + <td><p>Should messages be suppressed?</p></td> + </tr> + <tr> + <th>verbose</th> + <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give + detailed information about the C function being built.</p></td> + </tr> + </table> <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> +<dt>diffs</dt><dd><p>A vector of string representations of differential equations, + one for each modelling variable.</p></dd> + <dt>parms</dt><dd><p>A vector of parameter names occurring in the differential equations.</p></dd> + <dt>map</dt><dd><p>A list containing named character vectors for each observed variable, specifying + the modelling variables by which it is represented.</p></dd> + <dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> + <dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be + represented by one.</p></dd> + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> @@ -170,8 +182,8 @@ 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 + <a href = 'http://esdac.jrc.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.europa.eu/projects/degradation-kinetics</a></p> +<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> @@ -193,7 +205,7 @@ <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>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file2ac5b2884c1.c 2> file2ac5b2884c1.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file70ea30edf42a.c 2> file70ea30edf42a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: |