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<meta property="og:title" content="Customise priors for outbreaker — custom_priors" />
<meta property="og:description" content="Priors can be specified in several ways in outbreaker2 (see details and
examples). The most flexible way to specify a prior is to provide a prior
function directly. This function must take an argument 'param', which is a
list which contains all the states of the parameters and augmented data. See
the documentation of create_param for more information." />




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    <h1>Customise priors for outbreaker</h1>
    
    <div class="hidden name"><code>custom_priors.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Priors can be specified in several ways in outbreaker2 (see details and
examples). The most flexible way to specify a prior is to provide a prior
function directly. This function must take an argument 'param', which is a
list which contains all the states of the parameters and augmented data. See
the documentation of <a href='create_param.html'>create_param</a> for more information.</p>
    </div>

    <pre class="usage"><span class='fu'>custom_priors</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span>

<span class='co'># S3 method for custom_priors</span>
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>...</th>
      <td><p>A list or a series of named, comma-separated functions
implementing priors. Each function must have a single argument, which
corresponds to a 'outbreaker_param' list.</p></td>
    </tr>
    <tr>
      <th>x</th>
      <td><p>an <code>outbreaker_config</code> object as returned by <code>create_config</code>.</p></td>
    </tr>
    </table>

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

    <p>A list of custom functions with class <code>custom_priors</code>. Values
    set to <code>NULL</code> will be ignored and default functions will be used
    instead.</p>
    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

    <p>There are three ways a user can specify priors:<br /></p>
<p>1) Default: this is what happens when the 'config' has default values of
prior parameters.<br />
2) Customized parameters: in this case, the prior functions are the default
ones from the package, but will use custom parameters, specified by the user
through <code><a href='create_config.html'>create_config</a></code>.<br /></p>
<p>3) Customized functions: in this case, prior functions themselves are
specified by the user, through the '...' argument of 'custom_priors'. The
requirements is that such functions must have either hard-coded parameters or
enclosed values. They will take a single argument which is a list containing
all model parameters with the class 'outbreaker_param'. ALL PRIORS functions
are expected to return values on a LOG SCALE.<br /></p>
<p>Priors currently used for the model are:</p><ul>
<li><p><code>mu</code> (mutation rate): default function is an exponential
distribution implemented in <code>outbreaker:::cpp_prior_mu</code>. New prior
functions should use <code>x$mu</code> to refer to the current value of <code>mu</code>,
assuming their argument is called <code>x</code>.</p></li>
<li><p><code>pi</code> (reporting probability): default function is a beta
distribution implemented in <code>outbreaker:::cpp_prior_pi</code>. New prior
functions should use <code>x$pi</code> to refer to the current value of <code>pi</code>,
assuming their argument is called <code>x</code>.</p></li>
<li><p><code>eps</code> (contact reporting coverage): default function is a beta
distribution implemented in <code>outbreaker:::cpp_prior_eps</code>. New prior
functions should use <code>x$eps</code> to refer to the current value of <code>eps</code>,
assuming their argument is called <code>x</code>.</p></li>
<li><p><code>lambda</code> (non-infectious contact rate): default function is a
beta distribution implemented in <code>outbreaker:::cpp_prior_lambda</code>. New
prior functions should use <code>x$lambda</code> to refer to the current value of
<code>lambda</code>, assuming their argument is called <code>x</code>.</p></li>
</ul>

    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>

    <div class='dont-index'><p>See <a href='http://www.repidemicsconsortium.org/outbreaker2/articles/customisation.html#customising-priors'>customization vignette</a> for detailed examples on how to customize priors.</p></div>
    <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'>## BASIC CONFIGURATION</span>
<span class='fu'>custom_priors</span><span class='op'>(</span><span class='op'>)</span>
</div><div class='output co'>#&gt; 
#&gt; 
#&gt;  ///// outbreaker custom priors ///
#&gt; 
#&gt; class: custom_priors list
#&gt; number of items: 4 
#&gt; 
#&gt; /// custom priors set to NULL (default used) //
#&gt; $mu
#&gt; NULL
#&gt; 
#&gt; $pi
#&gt; NULL
#&gt; 
#&gt; $eps
#&gt; NULL
#&gt; 
#&gt; $lambda
#&gt; NULL
#&gt; </div><div class='input'>

<span class='co'>## SPECIFYING PRIOR PARAMETERS</span>
<span class='co'>## - this will need to be passed to outbreaker</span>
<span class='va'>default_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'>new_config</span> <span class='op'>&lt;-</span> <span class='fu'><a href='create_config.html'>create_config</a></span><span class='op'>(</span>prior_mu <span class='op'>=</span> <span class='fl'>1e-5</span>,
                        prior_pi <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>

<span class='co'>## - to check the prior manually, default settings:</span>
<span class='va'>param</span> <span class='op'>&lt;-</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'>0.001</span>, pi <span class='op'>=</span> <span class='fl'>0.9</span><span class='op'>)</span>
<span class='fu'>outbreaker2</span><span class='fu'>:::</span><span class='fu'>cpp_prior_mu</span><span class='op'>(</span><span class='va'>param</span>, <span class='va'>default_config</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -0.001</div><div class='input'><span class='fu'>outbreaker2</span><span class='fu'>:::</span><span class='fu'>cpp_prior_pi</span><span class='op'>(</span><span class='va'>param</span>, <span class='va'>default_config</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 1.35434</div><div class='input'>
<span class='fu'>outbreaker2</span><span class='fu'>:::</span><span class='fu'>cpp_prior_mu</span><span class='op'>(</span><span class='va'>param</span>, <span class='va'>new_config</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -11.51293</div><div class='input'><span class='fu'>outbreaker2</span><span class='fu'>:::</span><span class='fu'>cpp_prior_pi</span><span class='op'>(</span><span class='va'>param</span>, <span class='va'>new_config</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 0.5877867</div><div class='input'>
<span class='co'>## these correspond to:</span>
<span class='fu'><a href='https://rdrr.io/r/stats/Exponential.html'>dexp</a></span><span class='op'>(</span><span class='fl'>0.001</span>, <span class='fl'>0.01</span>, log <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -4.60518</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/Beta.html'>dbeta</a></span><span class='op'>(</span><span class='fl'>0.9</span>, <span class='fl'>2</span>, <span class='fl'>1</span>, log <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 0.5877867</div><div class='input'>

<span class='co'>## SPECIFYING A PRIOR FUNCTION</span>

<span class='co'>## flat prior for pi between 0.5 and 1</span>
<span class='va'>f</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='op'>{</span><span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>pi</span> <span class='op'>&gt;</span> <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>}</span>
<span class='va'>priors</span> <span class='op'>&lt;-</span> <span class='fu'>custom_priors</span><span class='op'>(</span>pi <span class='op'>=</span> <span class='va'>f</span><span class='op'>)</span>
<span class='va'>priors</span> <span class='co'># this should be passed to outbreaker</span>
</div><div class='output co'>#&gt; 
#&gt; 
#&gt;  ///// outbreaker custom priors ///
#&gt; 
#&gt; class: custom_priors list
#&gt; number of items: 4 
#&gt; 
#&gt; /// custom priors set to NULL (default used) //
#&gt; $mu
#&gt; NULL
#&gt; 
#&gt; $eps
#&gt; NULL
#&gt; 
#&gt; $lambda
#&gt; NULL
#&gt; 
#&gt; /// custom priors //
#&gt; $pi
#&gt; function(x) {ifelse(x$pi &gt; 0.5, log(2), log(0))}
#&gt; &lt;environment: 0x00000000348b8158&gt;
#&gt; </div><div class='input'>
<span class='co'>## test the prior manually</span>
<span class='va'>priors</span><span class='op'>$</span><span class='fu'>pi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pi<span class='op'>=</span><span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 0.6931472</div><div class='input'><span class='va'>priors</span><span class='op'>$</span><span class='fu'>pi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pi<span class='op'>=</span><span class='fl'>.6</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] 0.6931472</div><div class='input'><span class='va'>priors</span><span class='op'>$</span><span class='fu'>pi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pi<span class='op'>=</span><span class='fl'>.2</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -Inf</div><div class='input'><span class='va'>priors</span><span class='op'>$</span><span class='fu'>pi</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pi<span class='op'>=</span><span class='fl'>.49</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; [1] -Inf</div><div class='input'>
</div></pre>
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