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    <h1>Access internal C++ rountines used in outbreaker2</h1>
    
    <div class="hidden name"><code>get_cpp_api.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function returns an environment containing all C++ functions (bound to R
using Rcpp) used for priors, likelihoods, and movements of parameters in
outbreaker2.</p>
    </div>

    <pre class="usage"><span class='fu'>get_cpp_api</span><span class='op'>(</span><span class='op'>)</span></pre>


    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>An environment containing Rcpp bindings to C++ functions used internally in
outbreaker2. All functions are named as cpp_[type]_[component], where 'type'
can be:</p>
<ul>
<li><p>'prior': prior computation</p></li>
<li><p>'ll':  likelihood computation</p></li>
<li><p>'move': movement of parameters or augmented data</p></li>
</ul>

<p>And where 'component' can be:</p>
<ul>
<li><p>'mu': (parameter) mutation rate</p></li>
<li><p>'pi': (parameter) reporting probability</p></li>
<li><p>'lambda': (parameter) non-infectious contact rate</p></li>
<li><p>'eps': (parameter) contact reporting coverage</p></li>
<li><p>'alpha': (augmented data) ancestries of the cases</p></li>
<li><p>'kappa': (augmented data) generation between cases on transmission
chains</p></li>
<li><p>'t_inf': (augmented data) dates of infections</p></li>
<li><p>'timing_infections': (likelihood component) timing between infectors and
infectees</p></li>
<li><p>'timing_sampling': (likelihood component) timing between infection and
reporting / isolation</p></li>
<li><p>'timing': (likelihood component) sum of the two timing components</p></li>
<li><p>'genetic': (likelihood component) genetic diversity accumulated along
transmission chains</p></li>
<li><p>'reporting': (likelihood component) reporting of cases</p></li>
<li><p>'all': (likelihood component) sum of all likelihood components</p></li>
<li><p>'swap_cases': (type of movement) swap infectors and infectees on a
transmission tree</p></li>
</ul>

<p>For a description of the arguments of these functions, see the Rcpp_API
vignette (<code><a href='../articles/Rcpp_API.html'>vignette("Rcpp_API", package = "outbreaker2")</a></code>).</p>
    <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2>

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

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'>
<span class='co'>## get functions in an environment</span>
<span class='va'>api</span> <span class='op'>&lt;-</span> <span class='fu'>get_cpp_api</span><span class='op'>(</span><span class='op'>)</span>
<span class='va'>api</span>
</div><div class='output co'>#&gt; &lt;environment: 0x000000003a142060&gt;</div><div class='input'>
<span class='co'>## check content of the environment</span>
<span class='fu'><a href='https://rdrr.io/r/base/ls.html'>ls</a></span><span class='op'>(</span><span class='va'>api</span><span class='op'>)</span>
</div><div class='output co'>#&gt;  [1] "cpp_ll_all"               "cpp_ll_contact"          
#&gt;  [3] "cpp_ll_genetic"           "cpp_ll_reporting"        
#&gt;  [5] "cpp_ll_timing"            "cpp_ll_timing_infections"
#&gt;  [7] "cpp_ll_timing_sampling"   "cpp_move_alpha"          
#&gt;  [9] "cpp_move_eps"             "cpp_move_kappa"          
#&gt; [11] "cpp_move_lambda"          "cpp_move_mu"             
#&gt; [13] "cpp_move_pi"              "cpp_move_swap_cases"     
#&gt; [15] "cpp_move_t_inf"           "cpp_prior_all"           
#&gt; [17] "cpp_prior_eps"            "cpp_prior_lambda"        
#&gt; [19] "cpp_prior_mu"             "cpp_prior_pi"            </div><div class='input'>
<span class='co'>## test the prior for mu</span>
<span class='fu'><a href='https://rdrr.io/r/base/args.html'>args</a></span><span class='op'>(</span><span class='va'>api</span><span class='op'>$</span><span class='va'>cpp_prior_mu</span><span class='op'>)</span>
</div><div class='output co'>#&gt; function (param, config, custom_function = NULL) 
#&gt; NULL</div><div class='input'>
<span class='va'>config</span> <span class='op'>&lt;-</span> <span class='fu'><a href='create_config.html'>create_config</a></span><span class='op'>(</span><span class='op'>)</span>

<span class='va'>api</span><span class='op'>$</span><span class='fu'>cpp_prior_mu</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>mu <span class='op'>=</span> <span class='fl'>0.00123</span><span class='op'>)</span>, <span class='va'>config</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -0.00123</div><div class='input'>
<span class='fu'><a href='https://rdrr.io/r/stats/Exponential.html'>dexp</a></span><span class='op'>(</span><span class='fl'>0.00123</span>, rate <span class='op'>=</span> <span class='va'>config</span><span class='op'>$</span><span class='va'>prior_mu</span>, log <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -0.00123</div><div class='input'>
</div></pre>
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