<!-- 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>Extract quantities from a model fitted with BayesHMM. — extract • BayesHMM</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/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" 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">

<!-- clipboard.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>

<!-- sticky kit -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>

<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>



<meta property="og:title" content="Extract quantities from a model fitted with BayesHMM. — extract" />

<meta property="og:description" content="The extract_* family of methods returns elements from a fit object (including fixed and estimated quantities, as well as internal elements of the fit object)." />
<meta name="twitter:card" content="summary" />



<!-- mathjax -->
<script src='https://mathjax.rstudio.com/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 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">
        <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">BayesHMM</a>
        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.0.1</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav">
        <li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../reference/index.html">Reference</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/introduction.html">An Introduction to BayesHMM</a>
    </li>
    <li>
      <a href="../articles/introduction2.html">An Introduction to BayesHMM</a>
    </li>
  </ul>
</li>
      </ul>
      
      <ul class="nav navbar-nav navbar-right">
        <li>
  <a href="https://github.com/luisdamiano/BayesHMM/">
    <span class="fa 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>Extract quantities from a model fitted with BayesHMM.</h1>
    <small class="dont-index">Source: <a href='https://github.com/luisdamiano/BayesHMM//blob/master/R/extract.R'><code>R/extract.R</code></a></small>
    <div class="hidden name"><code>extract.Rd</code></div>
    </div>

    <div class="ref-description">
    
    <p>The extract_* family of methods returns elements from a fit object (including fixed and estimated quantities, as well as internal elements of the fit object).</p>
    
    </div>

    
    <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>fit</th>
      <td><p>An object returned by either <code><a href='draw_samples.html'>draw_samples</a></code> or <code><a href='optimizing.html'>optimizing</a></code>.</p></td>
    </tr>
    <tr>
      <th>reduce</th>
      <td><p>A function to be applied to all the samples generated by one chain for each parameters (i.e. "within chain"). Useful if only one or more summary measures of the generated samples is needed (e.g. the median of the generated sample). The function may return one of more elements. In the former case, the dimension is dropped in the returned object (read the <em>Value</em> section below). Note that the user needs to supply a function as an argument, and not a character string with the name of the function.</p></td>
    </tr>
    <tr>
      <th>combine</th>
      <td><p>A function applied to all the extracted quantities as an ensemble. In other words, instead of returning a named list where each element is one quantity, it returns the value returned by the function applied to the whole list (<code>do.call</code>). Useful when all the elements of the list have the same dimension, possibly because it is used in conjunction with the <em>chain</em> and <em>reduce</em> arguments.</p></td>
    </tr>
    <tr>
      <th>chain</th>
      <td><p>Either "all" or any integer number between 1 and the number of chains M.</p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>Arguments to be passed to rstan's <code><a href='http://www.rdocumentation.org/packages/rstan/topics/stanfit-method-extract'>extract</a></code> if the object <em>fit</em> was returned by <code><a href='fit.html'>fit</a></code> or <code><a href='draw_samples.html'>draw_samples</a></code>.</p></td>
    </tr>
    </table>
    
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>The extract_* family is the safest way to access the generated samples (filtered probability <em>alpha</em>, smoothed probability <em>gamma</em>, most likely hidden path <em>zstar</em>, observation samples from the posterior predictive density <em>ypred</em>, hidden path samples from the posterior predictive density <em>zpred</em>, simulated observations <em>ysim</em>), the fixed pre-specified quantities (observations <em>y</em>, time series length <em>T</em>, number of hidden states <em>K</em>, dimension of the observation vector <em>R</em>), Markov-chain Monte Carlo specific information (convergence and posterior predictive diagnostics <em>diagnostics</em>, number of chains <em>n_chains</em>, total iterations <em>n_iterations</em>, warm-up iterations <em>n_warmup</em>, thinning <em>n_thin</em>, sample size <em>sample_size</em>), and other internal elements stored in a fit object (<code><a href='specify.html'>Specification</a></code> object <em>spec</em>, dataset in list format <em>data</em>, date <em>date</em>, time elapsed for fitting <em>time</em>, seed <em>seed</em>, path to the underlying Stan file <em>filename</em>). Except for MCMC-specific functions, these all work interchangeably with both Markov-chain Monte Carlo samples returned by <code><a href='draw_samples.html'>draw_samples</a></code> and maximum a posteriori estimates returned by <code><a href='optimizing.html'>optimizing</a></code>.</p>
    
    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p>The arguments <em>reduce</em>, <em>combine</em>, and <em>chain</em> are very convenient tools to minimize the amount of data management in your code. See <code><a href='extract_quantity.html'>extract_quantity</a></code> for an in-depth explanation on how these work.</p>
<p>Other extract: <code><a href='extract_K.html'>extract_K</a></code>,
  <code><a href='extract_R.html'>extract_R</a></code>, <code><a href='extract_T.html'>extract_T</a></code>,
  <code><a href='extract_alpha.html'>extract_alpha</a></code>, <code><a href='extract_data.html'>extract_data</a></code>,
  <code><a href='extract_filename.html'>extract_filename</a></code>,
  <code><a href='extract_gamma.html'>extract_gamma</a></code>, <code><a href='extract_model.html'>extract_model</a></code>,
  <code><a href='extract_obs_parameters.html'>extract_obs_parameters</a></code>,
  <code><a href='extract_parameters.html'>extract_parameters</a></code>,
  <code><a href='extract_spec.html'>extract_spec</a></code>, <code><a href='extract_ypred.html'>extract_ypred</a></code>,
  <code><a href='extract_ysim.html'>extract_ysim</a></code>, <code><a href='extract_y.html'>extract_y</a></code>,
  <code><a href='extract_zpred.html'>extract_zpred</a></code>, <code><a href='extract_zsim.html'>extract_zsim</a></code>,
  <code><a href='extract_zstar.html'>extract_zstar</a></code></p></div>
    

  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
    <h2>Contents</h2>
    <ul class="nav nav-pills nav-stacked">
      <li><a href="#arguments">Arguments</a></li>
      
      <li><a href="#details">Details</a></li>

      <li><a href="#see-also">See also</a></li>
          </ul>

  </div>
</div>

      <footer>
      <div class="copyright">
  <p>Developed by Luis Damiano, Michael Weylandt, Brian Peterson.</p>
</div>

<div class="pkgdown">
  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
</div>

      </footer>
   </div>

  

  </body>
</html>

