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diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html new file mode 100644 index 00000000..5b624893 --- /dev/null +++ b/docs/reference/mmkin.html @@ -0,0 +1,178 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mmkin. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/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> + <div class="container"> + <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"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function calls <code>mkinfit</code> on all combinations of models and datasets + specified in its first two arguments.</p> + + + <pre><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>models</dt> + <dd> + Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"), or an optionally named list of <code>mkinmod</code> + objects. + </dd> + <dt>datasets</dt> + <dd> + An optionally named list of datasets suitable as observed data for + <code>mkinfit</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>makeCluster</code> to be used for parallel + execution. + </dd> + <dt>&#8230;</dt> + <dd> + Further arguments that will be passed to <code>mkinfit</code>. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A matrix of <code>mkinfit</code> objects that can be indexed using the model + and dataset names as row and column indices.</p> + </div> + + <div class="See also"> + <h2>See also</h2> + + <p><code>[.mmkin</code> for subsetting, <code>plot.mmkin</code> for plotting.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> +<span class='co'># M1 = mkinsub("SFO", "M2"),</span> +<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</span> +<span class='co'># M1 = mkinsub("SFO", "M2"),</span> +<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span> +<span class='co'># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span> +<span class='co'># names(datasets) <- paste("Dataset", 1:3)</span> +<span class='co'># </span> +<span class='co'># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span> +<span class='co'># time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))</span> +<span class='co'># </span> +<span class='co'># time_default</span> +<span class='co'># time_1</span> +<span class='co'># </span> +<span class='co'># endpoints(fits[["SFO_lin", 2]])</span> +<span class='co'># </span> +<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span> +<span class='co'># plot(fits.0[1, ])</span> +<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span> +<span class='co'># plot(fits.0[, 1])</span> +<span class='co'># # Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='co'># # by plot.mkinfit</span> +<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span> +<span class='co'># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +<span class='co'># # allow to plot the observed variables separately</span> +<span class='co'># plot(fits.0[1, 1])</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> |