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diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f592af1c..2eefdc2e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -8,11 +8,13 @@ <title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,18 +34,17 @@ -<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> -<meta property="og:description" content="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. -For the definition of model types and their parameters, the equations given - in the FOCUS and NAFTA guidance documents are used." /> +<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> +<meta property="og:description" content="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." /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -114,7 +115,6 @@ For the definition of model types and their parameters, the equations given <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -136,49 +136,47 @@ For the definition of model types and their parameters, the equations given </div> <div class="ref-description"> - - <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> - + <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> </div> - <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> - + <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> <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 - 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.</p></td> + <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 +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.</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.</p></td> + <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.</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> + <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> @@ -186,44 +184,46 @@ For the definition of model types and their parameters, the equations given </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> + <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="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, among others,</p> +<dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for + each modelling variable.</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> + <dt>ll</dt><dd><p>The likelihood function, taking the parameter vector as the first argument.</p></dd> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>For the definition of model types and their parameters, the equations given +in the FOCUS and NAFTA guidance documents are used.</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> - + <p>The IORE submodel is not well tested for metabolites. 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, + <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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.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> - + 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> + <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'><a href='https://rdrr.io/r/base/list.html'>list</a></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> @@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given <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 file663b71dc323f.c 2> file663b71dc323f.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: @@ -260,7 +260,7 @@ For the definition of model types and their parameters, the equations given #> 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><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'># If we have several parallel metabolites </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='no'>m_synth_DFOP_par</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'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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>), @@ -276,13 +276,10 @@ For the definition of model types and their parameters, the equations given <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="#details">Details</a></li> <li><a href="#note">Note</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> |