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diff --git a/docs/mmkin.html b/docs/mmkin.html deleted file mode 100644 index 5924d3d5..00000000 --- a/docs/mmkin.html +++ /dev/null @@ -1,172 +0,0 @@ -<!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>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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