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| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-27 06:06:08 +0200 |
| commit | a77a10ea6c607346778ba0700b3b66ac393101a2 (patch) | |
| tree | e91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/mkinmod.html | |
| parent | 675a733fa2acc08daabb9b8b571c7d658f281f73 (diff) | |
Create up to date pkgdown docs in development mode
Diffstat (limited to 'docs/dev/reference/mkinmod.html')
| -rw-r--r-- | docs/dev/reference/mkinmod.html | 320 |
1 files changed, 320 insertions, 0 deletions
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Instead of specifying several expressions, a +list of lists can be given in the speclist argument." /> + + +<meta name="robots" content="noindex"> + +<!-- 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> + +<!--[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 data-spy="scroll" data-target="#toc"> + <div class="container template-reference-topic"> + <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" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <span class="navbar-brand"> + <a class="navbar-link" href="../index.html">mkin</a> + <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="../articles/web_only/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> + <li> + <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </li> + <li> + <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + </li> + </ul> +</li> +<li> + <a href="../news/index.html">News</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Function to set up a kinetic model with one or more state variables</h1> + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small> + <div class="hidden name"><code>mkinmod.Rd</code></div> + </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> + </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'>"max"</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> + </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> + </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, 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>deg_func</dt><dd><p>If generated, a function containing the solution of the degradation +model.</p></dd> +<dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be +represented by one.</p></dd> +<dt>cf</dt><dd><p>If generated, a compiled function calculating the derivatives as +returned by cfunction.</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 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, +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> + + <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> +<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='mkinsub.html'>mkinsub</a></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'><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>))</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'># \dontrun{</span> +<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</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'><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='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</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>))</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'># Show details of creating the C function</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'><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 file1bc3f55ac46.c 2> file1bc3f55ac46.c.err.txt +#> Program source: +#> 1: #include <R.h> +#> 2: +#> 3: +#> 4: static double parms [3]; +#> 5: #define k_parent parms[0] +#> 6: #define f_parent_to_m1 parms[1] +#> 7: #define k_m1 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 * y[0]; +#> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * 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'># (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>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + +<span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, + <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='co'># }</span></div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + |