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<title>outbreaker2: a platform for disease outbreak reconstruction — outbreaker_package • outbreaker2</title>





  
  

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<meta property="og:title" content="outbreaker2: a platform for disease outbreak reconstruction — outbreaker_package" />





  
  

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<meta property="og:description" content="This package provides a statistical platform for reconstructing transmission





  
  

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trees ('who infects whom') in densely sampled disease outbreaks. It





  
  

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reimplements, as a particular case, the model of 'outbreaker' (see





  
  

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references). 'outbreaker2' extends and replaces 'outbreaker'. " />





  
  

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      <a href="../articles/customisation.html">Using custom priors, likelihood, or movements in outbreaker2</a>





  
  

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      <a href="../articles/introduction.html">Introduction to outbreaker2</a>





  
  

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      <a href="../articles/overview.html">outbreaker2: package overview</a>





  
  

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      <a href="../articles/Rcpp_API.html">outbreaker2: Rcpp API</a>





  
  

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    <h1>outbreaker2: a platform for disease outbreak reconstruction</h1>





  
  

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    <div class="hidden name"><code>outbreaker_package.Rd</code></div>





  
  

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    </div>





  
  

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    <div class="ref-description">





  
  

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    <p>This package provides a statistical platform for reconstructing transmission





  
  

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trees ('who infects whom') in densely sampled disease outbreaks. It





  
  

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reimplements, as a particular case, the model of 'outbreaker' (see





  
  

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references). 'outbreaker2' extends and replaces 'outbreaker'. <br /></p>





  
  

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    </div>





  
  

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    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>





  
  

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    <p>The emphasis of 'outbreaker2' is on modularity, which enables customisation





  
  

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of priors, likelihoods and even movements of parameters and augmented data by





  
  

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the user. This the dedicated vignette on this topic





  
  

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<code>vignette("outbreaker2_custom")</code>.<br /></p>





  
  

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<p>The main functions of the package are:</p><ul>





  
  

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<li><p><code><a href='outbreaker.html'>outbreaker</a></code>: main function to run analyses</p></li>





  
  

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<li><p><code><a href='outbreaker_data.html'>outbreaker_data</a></code>: function to process input data</p></li>





  
  

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<li><p><code><a href='create_config.html'>create_config</a></code>: function to create default and customise





  
  

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configuration settings</p></li>





  
  

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<li><p><code><a href='custom_priors.html'>custom_priors</a></code>: function to specify customised prior





  
  

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functions</p></li>





  
  

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<li><p><code><a href='custom_likelihoods.html'>custom_likelihoods</a></code>: function to specify customised likelihoods





  
  

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functions</p></li>





  
  

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<li><p><code><a href='custom_moves.html'>custom_moves</a></code>: function to create default and customise movement





  
  

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functions</p></li>





  
  

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</ul>





  
  

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    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>





  
  

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    <p>Thibaut Jombart <a href='mailto:thibautjombart@gmail.com'>thibautjombart@gmail.com</a></p>





  
  

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  <p>Developed by Thibaut Jombart, Finlay Campbell, Rich Fitzjohn.</p>





  
  

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