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        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span>





  
  

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





  
  

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      <h1 data-toc-skip>Changelog <small></small></h1>





  
  

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    <div id="outbreaker2-112-2021-01-25" class="section level1">





  
  

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<h1 class="page-header" data-toc-text="1.1.2">





  
  

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<a href="#outbreaker2-112-2021-01-25" class="anchor"></a>outbreaker2 1.1.2 (2021-01-25)<small> Unreleased </small>





  
  

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<h3 class="hasAnchor">





  
  

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<a href="#new-features" class="anchor"></a>New features</h3>





  
  

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<li>Custom likelihoods now support local likelihood calculations via the optional <code>i</code> argument; this will speed up likelihood calculations by avoiding global calculations where these are unnecessary</li>





  
  

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<a href="#bug-fixes" class="anchor"></a>Bug fixes</h3>





  
  

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<li>Random index shuffling in cpp_move_swap_cases to ensure correct mixing</li>





  
  

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<li>Negative serial intervals now allowed in can_be_ances</li>





  
  

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<li>ID labels fix in plotting functions</li>





  
  

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<p><br><br></p>





  
  

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    <div id="outbreaker2-111-2020-01-31" class="section level1">





  
  

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<h1 class="page-header" data-toc-text="1.1.1">





  
  

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<a href="#outbreaker2-111-2020-01-31" class="anchor"></a>outbreaker2 1.1.1 (2020-01-31)<small> 2020-02-07 </small>





  
  

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</h1>





  
  

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<div id="bug-fixes-1" class="section level3">





  
  

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<h3 class="hasAnchor">





  
  

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<a href="#bug-fixes-1" class="anchor"></a>Bug fixes</h3>





  
  

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<ul>





  
  

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<li>Fixed uninitialized variable use</li>





  
  

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<li>Updated email addresses</li>





  
  

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<p><br><br></p>





  
  

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    <div id="outbreaker2-110-2019-06-06" class="section level1">





  
  

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<h1 class="page-header" data-toc-text="1.1.0">





  
  

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<a href="#outbreaker2-110-2019-06-06" class="anchor"></a>outbreaker2 1.1.0 (2019-06-06)<small> 2019-06-13 </small>





  
  

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</h1>





  
  

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<h3 class="hasAnchor">





  
  

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<a href="#bug-fixes-2" class="anchor"></a>Bug fixes</h3>





  
  

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<ul>





  
  

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<li>The genetic likelihood of the <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003457">original <em>outbreaker</em> paper</a> was found to contain a minor mistake in accounting for unobserved generations of infection. As of June 7th 2019, <em>outbreaker2</em> will use the correct genetic likelihood published <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006930">here</a>.</li>





  
  

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<h3 class="hasAnchor">





  
  

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<a href="#new-features-1" class="anchor"></a>New features</h3>





  
  

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<ul>





  
  

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<li>





  
  

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<em>outbreaker2</em> now accepts <code>epicontacts</code> objects for contact data</li>





  
  

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<li>Contact tracing data can be directed or not by toggling <code>ctd_directed</code>





  
  

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</li>





  
  

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<li>Cyclical consensus trees can now be avoided by using <code>method = 'decyle'</code> in <code>summary.outbreaker_chains</code>





  
  

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</li>





  
  

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<li>Added support for case-labelling in <code>plot.outbreaker_chains</code>





  
  

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<li>Added progress bar</li>





  
  

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<p><br><br></p>





  
  

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    <div id="outbreaker2-101-2018-03-06" class="section level1">





  
  

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<h1 class="page-header" data-toc-text="1.0.1">





  
  

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<a href="#outbreaker2-101-2018-03-06" class="anchor"></a>outbreaker2 1.0.1 (2018-03-06)<small> 2018-03-06 </small>





  
  

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</h1>





  
  

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<div id="minor-bug-fixes" class="section level3">





  
  

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<h3 class="hasAnchor">





  
  

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<a href="#minor-bug-fixes" class="anchor"></a>Minor bug fixes</h3>





  
  

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<ul>





  
  

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<li>Fixed convolution operator to keep values in log space with high kappa (thanks to <a href="https://github.com/gtonkinhill/">@gtonkinhill</a>)</li>





  
  

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<li>C++ garbage collection fix</li>





  
  

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<p><br><br></p>





  
  

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    <div id="outbreaker2-100-2017-11-24" class="section level1">





  
  

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<h1 class="page-header" data-toc-text="1.0.0">





  
  

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<a href="#outbreaker2-100-2017-11-24" class="anchor"></a>outbreaker2 1.0.0 (2017-11-24)<small> Unreleased </small>





  
  

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<div id="first-version-of-outbreaker2" class="section level3">





  
  

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<a href="#first-version-of-outbreaker2" class="anchor"></a>First version of outbreaker2!</h3>





  
  

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<ul>





  
  

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<li><p>This package re-implements and generalises the package <a href="https://CRAN.R-project.org/package=outbreaker"><em>outbreaker</em></a></p></li>





  
  

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<li><p>It provides various functions to process input data, specify settings of the method, and even specify custom priors, likelihoods, or movement functions.</p></li>





  
  

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<li><p>Outputs of the main function <code>outbreaker</code> have a dedicated class extending the regular <code>data.frame</code>, with <code>print</code>, <code>summary</code> and <code>plot</code> methods.</p></li>





  
  

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<li><p>Its engine is written in C++, interfaced via Rcpp.</p></li>





  
  

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<li><p>Its C++ API is accessible via the function <code><a href="../reference/get_cpp_api.html">get_cpp_api()</a></code>.</p></li>





  
  

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<li><p>Functionalities are documented in 4 vignettes.</p></li>





  
  

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





  
  

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