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diff --git a/docs/mmkin.html b/docs/mmkin.html new file mode 100644 index 00000000..5924d3d5 --- /dev/null +++ b/docs/mmkin.html @@ -0,0 +1,172 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>mmkin. 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> + Fit one or more kinetic models with one or more state variables to one or more datasets +</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="functioncall"><a href='mmkin.html'>mmkin</a></span><span class="keyword">(</span><span class="symbol">models</span><span class="keyword">,</span> <span class="symbol">datasets</span><span class="keyword">,</span> + <span class="argument">cores</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/Round'>round</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/parallel/topics/detectCores'>detectCores</a></span><span class="keyword">(</span><span class="keyword">)</span><span class="keyword">/</span><span class="number">2</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">cluster</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> + + <h2>Arguments</h2> + <dl> + <dt>models</dt> + <dd> + Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code> + objects. + </dd> + <dt>datasets</dt> + <dd> + An optionally named list of datasets suitable as observed data for + <code><a href='mkinfit.html'>mkinfit</a></code>. + </dd> + <dt>cores</dt> + <dd> + The number of cores to be used for multicore processing. This is only + used when the <code>cluster</code> argument is <code>NULL</code>. + </dd> + <dt>cluster</dt> + <dd> + A cluster as returned by <code><a href='http://www.rdocumentation.org/packages/parallel/topics/makeCluster'>makeCluster</a></code> to be used for parallel + execution. + </dd> + <dt>...</dt> + <dd> + Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>. + </dd> + </dl> + + <div class="Description"> + <h2>Description</h2> + + <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and datasets + specified in its first two arguments.</p> + + </div> + + <div class="Value"> + <h2>Value</h2> + + <p><dl> + A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model + and dataset names as row and column indices. +</dl></p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="comment">## Not run: ------------------------------------</span> +<span class="comment"># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> +<span class="comment"># M1 = mkinsub("SFO", "M2"),</span> +<span class="comment"># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class="comment"># </span> +<span class="comment"># m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</span> +<span class="comment"># M1 = mkinsub("SFO", "M2"),</span> +<span class="comment"># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class="comment"># </span> +<span class="comment"># models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span> +<span class="comment"># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span> +<span class="comment"># names(datasets) <- paste("Dataset", 1:3)</span> +<span class="comment"># </span> +<span class="comment"># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span> +<span class="comment"># time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))</span> +<span class="comment"># </span> +<span class="comment"># time_default</span> +<span class="comment"># time_1</span> +<span class="comment"># </span> +<span class="comment"># endpoints(fits[["SFO_lin", 2]])</span> +<span class="comment"># </span> +<span class="comment"># # Plot.mkinfit handles rows or columns of mmkin result objects</span> +<span class="comment"># plot(fits.0[1, ])</span> +<span class="comment"># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span> +<span class="comment"># plot(fits.0[, 1])</span> +<span class="comment"># # Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class="comment"># # by plot.mkinfit</span> +<span class="comment"># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span> +<span class="comment"># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +<span class="comment"># # allow to plot the observed variables separately</span> +<span class="comment"># plot(fits.0[1, 1])</span> +<span class="comment">## ---------------------------------------------</span></div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>mmkin</li> + </ul> + <ul> + <li> optimize </li> + </ul> --> + + <h2>See also</h2> + <p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.</p> + + + + <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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