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      <h1 data-toc-skip>outbreaker2: package overview</h1>

                        <h4 class="author">Thibaut Jombart</h4>

            

            <h4 class="date">2021-02-09</h4>

      

      

      <div class="hidden name"><code>overview.Rmd</code></div>



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<p><em>oubtreaker2</em> provides a platform for reconstructing densely sampled outbreaks using epidemiological and genetic data. See <a href="introduction.html">introduction vignette</a> for a worked example.</p>

<p><br></p>

<div id="installing-the-package" class="section level1">

<h1 class="hasAnchor">

<a href="#installing-the-package" class="anchor"></a>Installing the package</h1>

<p>To install the current stable, CRAN version of the package, type:</p>

<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"outbreaker2"</span><span class="op">)</span></code></pre></div>

<p>To benefit from the latest features and bug fixes, install the development, <em>github</em> version of the package using:</p>

<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/remote-reexports.html">install_github</a></span><span class="op">(</span><span class="st">"reconhub/outbreaker2"</span><span class="op">)</span></code></pre></div>

<p>Note that this requires the package <em>devtools</em> installed.</p>

<p><br></p>

</div>

<div id="main-visible-functions-of-the-package" class="section level1">

<h1 class="hasAnchor">

<a href="#main-visible-functions-of-the-package" class="anchor"></a>Main visible functions of the package</h1>

<p>The main functions of the package include:</p>

<ul>

<li><p><strong><code>outbreaker</code></strong>: the returned object is an instance of the (S3) class <em>outbreaker_chains</em>.</p></li>

<li><p><strong><code>plot</code></strong>: this method (see <code><a href="../reference/print.outbreaker_chains.html">?plot.outbreaker_chains</a></code> for details) plots <em>outbreaker_chains</em> objects.</p></li>

<li><p><strong><code>summary</code></strong>: this method (see <code><a href="../reference/print.outbreaker_chains.html">?summary.outbreaker_chains</a></code> for details) provides summaries for the various outputs of <em>outbreaker2</em>, stored in an <em>outbreaker_chains</em> object.</p></li>

<li><p><strong><code>outbreaker_data</code></strong>: function processing input data.</p></li>

<li><p><strong><code>create_config</code></strong>: function creating default settings, also used for specifying customised settings for <em>outbreaker2</em>.</p></li>

<li><p><strong><code>custom_priors</code></strong>: function used for specifying customised functions to be used as priors in <em>outbreaker2</em>.</p></li>

<li><p><strong><code>custom_likelihoods</code></strong>: function used for specifying customised functions to be used for likelihood computation in <em>outbreaker2</em>.</p></li>

<li><p><strong><code>custom_moves</code></strong>: function used for specifying customised functions to be used for moving parameters and augmented data in <em>outbreaker2</em>.</p></li>

</ul>

<p><br></p>

</div>

<div id="main-internal-functions" class="section level1">

<h1 class="hasAnchor">

<a href="#main-internal-functions" class="anchor"></a>Main internal functions</h1>

<p><em>outbreaker2</em> uses many functions internally which are not visible to the user when loading the package. However, some of these functions will be useful when designing custom likelihoods or movement functions, or when contributing code. The most useful ones are C++ functions bound to R using Rcpp. The list of these functions is:</p>

<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">

<code class="sourceCode R"><span class="va">env</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/ns-internal.html">asNamespace</a></span><span class="op">(</span><span class="st">"outbreaker2"</span><span class="op">)</span>

<span class="fu"><a href="https://rdrr.io/r/base/ls.html">ls</a></span><span class="op">(</span>envir <span class="op">=</span> <span class="va">env</span>, pattern <span class="op">=</span> <span class="st">"^cpp"</span><span class="op">)</span>  </code></pre></div>

<pre><code>##  [1] "cpp_are_possible_ancestors"    "cpp_find_descendents"         

##  [3] "cpp_find_local_cases"          "cpp_get_n_mutations"          

##  [5] "cpp_ll_all"                    "cpp_ll_contact"               

##  [7] "cpp_ll_genetic"                "cpp_ll_reporting"             

##  [9] "cpp_ll_timing"                 "cpp_ll_timing_infections"     

## [11] "cpp_ll_timing_sampling"        "cpp_lookup_sequenced_ancestor"

## [13] "cpp_move_alpha"                "cpp_move_eps"                 

## [15] "cpp_move_kappa"                "cpp_move_lambda"              

## [17] "cpp_move_mu"                   "cpp_move_pi"                  

## [19] "cpp_move_swap_cases"           "cpp_move_t_inf"               

## [21] "cpp_pick_possible_ancestor"    "cpp_prior_all"                

## [23] "cpp_prior_eps"                 "cpp_prior_lambda"             

## [25] "cpp_prior_mu"                  "cpp_prior_pi"                 

## [27] "cpp_sample1"                   "cpp_swap_cases"</code></pre>

<p>See the vignette on <a href="Rcpp_API.html">Rcpp API</a> for a detail of these functions.</p>

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