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      <h1 data-toc-skip>outbreaker2: Rcpp API</h1>
                        <h4 class="author">Thibaut Jombart</h4>
            
            <h4 class="date">2021-02-09</h4>
      
      
      <div class="hidden name"><code>Rcpp_API.Rmd</code></div>

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<div id="list-of-available-functions" class="section level1">
<h1 class="hasAnchor">
<a href="#list-of-available-functions" class="anchor"></a>List of available functions</h1>
<p>The C++ functions bound to R via Rcpp used in <em>outbreaker2</em> for priors, likelihoods and movements are not visible to the user, as they are not exported by the package. However, advanced users can access these functions using <code><a href="../reference/get_cpp_api.html">get_cpp_api()</a></code>, which returns an environment with all relevant functions:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va">outbreaker2</span><span class="op">)</span> 

<span class="co">## get all functions in an environment</span>
<span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/get_cpp_api.html">get_cpp_api</a></span><span class="op">(</span><span class="op">)</span>
<span class="va">x</span></code></pre></div>
<pre><code>## &lt;environment: 0x0000000022e6d350&gt;</code></pre>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co">## check content</span>
<span class="fu"><a href="https://rdrr.io/r/base/ls.html">ls</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></code></pre></div>
<pre><code>##  [1] "cpp_ll_all"               "cpp_ll_contact"          
##  [3] "cpp_ll_genetic"           "cpp_ll_reporting"        
##  [5] "cpp_ll_timing"            "cpp_ll_timing_infections"
##  [7] "cpp_ll_timing_sampling"   "cpp_move_alpha"          
##  [9] "cpp_move_eps"             "cpp_move_kappa"          
## [11] "cpp_move_lambda"          "cpp_move_mu"             
## [13] "cpp_move_pi"              "cpp_move_swap_cases"     
## [15] "cpp_move_t_inf"           "cpp_prior_all"           
## [17] "cpp_prior_eps"            "cpp_prior_lambda"        
## [19] "cpp_prior_mu"             "cpp_prior_pi"</code></pre>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co">## all functions are Rcpp bindings to a C++ function</span>
<span class="va">x</span><span class="op">$</span><span class="va">cpp_ll_all</span></code></pre></div>
<pre><code>## function (data, param, i = NULL, custom_functions = NULL) 
## {
##     .Call(`_outbreaker2_cpp_ll_all`, data, param, i, custom_functions)
## }
## &lt;bytecode: 0x0000000022e6dd98&gt;
## &lt;environment: namespace:outbreaker2&gt;</code></pre>
</div>
<div id="function-signatures" class="section level1">
<h1 class="hasAnchor">
<a href="#function-signatures" class="anchor"></a>Function signatures</h1>
<p>These functions take the following arguments:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">list_args</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html">lapply</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">args</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/ls.html">ls</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">]</span>
<span class="va">list_args</span></code></pre></div>
<pre><code>## $cpp_ll_all
## function (data, param, i = NULL, custom_functions = NULL) 
## NULL
## 
## $cpp_ll_contact
## function (data, param, i = NULL, custom_function = NULL) 
## NULL
## 
## $cpp_ll_genetic
## function (data, param, i = NULL, custom_function = NULL) 
## NULL
## 
## $cpp_ll_reporting
## function (data, param, i = NULL, custom_function = NULL) 
## NULL
## 
## $cpp_ll_timing
## function (data, param, i = NULL, custom_functions = NULL) 
## NULL
## 
## $cpp_ll_timing_infections
## function (data, param, i = NULL, custom_function = NULL) 
## NULL
## 
## $cpp_ll_timing_sampling
## function (data, param, i = NULL, custom_function = NULL) 
## NULL
## 
## $cpp_move_alpha
## function (param, data, list_custom_ll = NULL) 
## NULL
## 
## $cpp_move_eps
## function (param, data, config, custom_ll = NULL, custom_prior = NULL) 
## NULL
## 
## $cpp_move_kappa
## function (param, data, config, list_custom_ll = NULL) 
## NULL
## 
## $cpp_move_lambda
## function (param, data, config, custom_ll = NULL, custom_prior = NULL) 
## NULL
## 
## $cpp_move_mu
## function (param, data, config, custom_ll = NULL, custom_prior = NULL) 
## NULL
## 
## $cpp_move_pi
## function (param, data, config, custom_ll = NULL, custom_prior = NULL) 
## NULL
## 
## $cpp_move_swap_cases
## function (param, data, list_custom_ll = NULL) 
## NULL
## 
## $cpp_move_t_inf
## function (param, data, list_custom_ll = NULL) 
## NULL
## 
## $cpp_prior_all
## function (param, config, custom_functions = NULL) 
## NULL
## 
## $cpp_prior_eps
## function (param, config, custom_function = NULL) 
## NULL
## 
## $cpp_prior_lambda
## function (param, config, custom_function = NULL) 
## NULL
## 
## $cpp_prior_mu
## function (param, config, custom_function = NULL) 
## NULL
## 
## $cpp_prior_pi
## function (param, config, custom_function = NULL) 
## NULL</code></pre>
<p>Arguments are detailed in the next section.</p>
</div>
<div id="arguments" class="section level1">
<h1 class="hasAnchor">
<a href="#arguments" class="anchor"></a>Arguments</h1>
<p>Arguments of the Rcpp-bound C++ functions are:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">list_formals</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html">lapply</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">formals</span><span class="op">)</span>
<span class="va">args</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sort.html">sort</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unique.html">unique</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/unlist.html">unlist</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html">lapply</a></span><span class="op">(</span><span class="va">list_formals</span>, <span class="va">names</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>
<span class="va">args</span></code></pre></div>
<pre><code>## [1] "config"           "custom_function"  "custom_functions" "custom_ll"       
## [5] "custom_prior"     "data"             "i"                "list_custom_ll"  
## [9] "param"</code></pre>
<ul>
<li><p><strong><code>alpha</code></strong>: a vector of integers of length ‘N’ (number of cases), indicating infectors of each case, with values from 1 to N; missing values should be <code>NA</code></p></li>
<li><p><strong><code>config</code></strong>: a list containing configuration settings as returned by <code>create_config</code></p></li>
<li><p><strong><code>custom_function</code></strong>: a R function for a custom prior, with a single argument, which must be a list of parameters and augmented data with the class <code>outbreaker_param</code>; returned values must be <strong>on the log scale</strong></p></li>
<li><p><strong><code>custom_functions</code></strong>: a list of R functions obeying the rules of <code>custom_function</code>, named according to the priors; currently available names are:</p></li>
</ul>
<pre><code>## [1] "eps"    "lambda" "mu"     "pi"</code></pre>
<ul>
<li><p><strong><code>custom_ll</code></strong>: a R function for a custom likelihood, taking two arguments: <code>data</code> (see <code>data</code>), and <code>param</code> (see <code>param</code>)</p></li>
<li><p><strong><code>custom_prior</code></strong>: same as <code>custom_function</code></p></li>
<li><p><strong><code>data</code></strong>: a valid ‘outbreaker_data’ list</p></li>
<li><p><strong><code>i</code></strong>: an integer scalar indicating the index of a case, from 1 to N (number of cases)</p></li>
<li><p><strong><code>list_custom_ll</code></strong>: a list of R functions obeying the rules of <code>custom_ll</code>, named according to the computed likelihood component; available names are:</p></li>
</ul>
<pre><code>## [1] "contact"           "genetic"           "reporting"        
## [4] "timing_infections" "timing_sampling"</code></pre>
<ul>
<li><p><strong><code>param</code></strong>: a list containing parameters and augmented data with the class <code>outbreaker_param</code></p></li>
<li><p><strong><code>t_inf</code></strong>: a vector of integers of length N (number of cases), indicating infection dates of each case; missing values should be <code>NA</code></p></li>
<li><p><strong><code>x</code></strong>: a vector of integers to be sampled from</p></li>
</ul>
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