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<h1>Set and check parameter settings of outbreaker</h1>
<div class="hidden name"><code>create_config.Rd</code></div>
</div>
<div class="ref-description">
<p>This function defines settings for outbreaker. It takes a list of named
items as input, performs various checks, set defaults where arguments are
missing, and return a correct list of settings. If no input is given, it
returns the default settings.</p>
</div>
<pre class="usage"><span class='fu'>create_config</span><span class='op'>(</span><span class='va'>...</span>, data <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='co'># S3 method for outbreaker_config</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>further arguments to be passed to other methods</p></td>
</tr>
<tr>
<th>data</th>
<td><p>an optional list of data items as returned by
<code>outbreaker_data</code>; if provided, this allows for further checks of
the outbreaker setings.</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="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Acceptables arguments for ... are:</p>
<dl>
<dt>init_tree</dt><dd><p>the tree used to initialize the MCMC. Can be either a
character string indicating how this tree should be computed, or a vector of
integers corresponding to the tree itself, where the i-th value corresponds
to the index of the ancestor of 'i' (i.e., <code>init.tree[i]</code> is the
ancestor of case <code>i</code>). Accepted character strings are "seqTrack" (uses
seqTrack algorithm to generate the initial tree - see function
<code>seqTrack</code> in the package <code>adegenet</code>), "random" (ancestor randomly
selected from preceding cases), and "star" (all cases coalesce to the first
case). Note that for SeqTrack, all cases should have been sequenced.</p></dd>
<dt>init_alpha</dt><dd><p>a vector of integers indicating the initial values of
alpha, where the i-th value indicates the ancestor of case 'i'; defaults to
<code>NULL</code>, in which ancestries are defined from <code>init_tree</code>.</p></dd>
<dt>init_kappa</dt><dd><p>a (recycled) vector of integers indicating the initial
values of kappa; defaults to 1.</p></dd>
<dt>init_t_inf</dt><dd><p>a vector of integers indicating the initial values of
<code>t_inf</code>, i.e. dates of infection; defaults to <code>NULL</code>, in which case
the most likely <code>t_inf</code> will be determined from the delay to
reporting/symptoms distribution, and the dates of reporting/symptoms,
provided in <code>data</code>.</p></dd>
<dt>init_mu</dt><dd><p>initial value for the mutation rates</p></dd>
<dt>init_pi</dt><dd><p>initial value for the reporting probability</p></dd>
<dt>init_eps</dt><dd><p>initial value for the contact reporting coverage</p></dd>
<dt>init_lambda</dt><dd><p>initial value for the non-infectious contact rate</p></dd>
<dt>n_iter</dt><dd><p>an integer indicating the number of iterations in the MCMC,
including the burnin period</p></dd>
<dt>move_alpha</dt><dd><p>a vector of logicals indicating, for each case, if the
ancestry should be estimated ('moved' in the MCMC), or not, defaulting to
TRUE; the vector is recycled if needed.</p></dd>
<dt>move_t_inf</dt><dd><p>a vector of logicals indicating, for each case, if the
dates of infection should be estimated ('moved' in the MCMC), or not,
defaulting to TRUE; the vector is recycled if needed.</p></dd>
<dt>move_mu</dt><dd><p>a logical indicating whether the mutation rates
should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd>
<dt>move_pi</dt><dd><p>a logical indicating whether the reporting probability
should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd>
<dt>move_eps</dt><dd><p>a logical indicating whether the contact reporting coverage
should be estimated ('moved' in the MCMC), or not at all, defaulting to
TRUE.</p></dd>
<dt>move_lambda</dt><dd><p>a logical indicating whether the non-infectious contact
rate should be estimated ('moved' in the MCMC), or not at all, defaulting to
TRUE.</p></dd>
<dt>move_kappa</dt><dd><p>a logical indicating whether the number of generations
between two successive cases should be estimated ('moved' in the MCMC), or
not, all defaulting to TRUE.</p></dd>
<dt>move_pi</dt><dd><p>a logical indicating whether the reporting probability
should be estimated ('moved' in the MCMC), or not, all defaulting to TRUE.</p></dd>
<dt>n_iter</dt><dd><p>the number of iterations of the MCMC</p></dd>
<dt>sample_every</dt><dd><p>the frequency at which MCMC samples are retained for the
output</p></dd>
<dt>sd_mu</dt><dd><p>the standard deviation for the Normal proposal for the mutation
rates</p></dd>
<dt>sd_pi</dt><dd><p>the standard deviation for the Normal proposal for the reporting
probability</p></dd>
<dt>sd_eps</dt><dd><p>the standard deviation for the Normal proposal for the
contact reporting coverage</p></dd>
<dt>sd_lambda</dt><dd><p>the standard deviation for the Normal proposal for the
non-infectious contact rate</p></dd>
<dt>prop_alpha_move</dt><dd><p>the proportion of ancestries to move at each iteration
of the MCMC</p></dd>
<dt>prop_t_inf_move</dt><dd><p>the proportion of infection dates to move at each
iteration of the MCMC</p></dd>
<dt>batch_size</dt><dd><p>the size of the batch of random number pre-generated</p></dd>
<dt>paranoid</dt><dd><p>a logical indicating if the paranoid mode should be used;
this mode is used for performing additional tests during outbreaker; it makes
computations substantially slower and is mostly used for debugging purposes.</p></dd>
<dt>min_date</dt><dd><p>earliest infection date possible, expressed as days since the
first sampling</p></dd>
<dt>max_kappa</dt><dd><p>an integer indicating the largest number of generations
between any two linked cases; defaults to 5</p></dd>
<dt>prior_mu</dt><dd><p>a numeric value indicating the rate of the exponential prior
for the mutation rate 'mu'</p></dd>
<dt>prior_pi</dt><dd><p>a numeric vector of length 2 indicating the first and second
parameter of the beta prior for the reporting probability 'pi'</p></dd>
<dt>prior_eps</dt><dd><p>a numeric vector of length 2 indicating the first and second
parameter of the beta prior for the contact reporting coverage 'eps'</p></dd>
<dt>prior_lambda</dt><dd><p>a numeric vector of length 2 indicating the first and
second parameter of the beta prior for the non-infectious contact rate
'lambda'</p></dd>
<dt>ctd_directed</dt><dd><p>a logical indicating if the contact tracing data is
directed or not. If yes, the first column represents the infector and the
second column the infectee. If ctd is provided as an epicontacts objects,
directionality will be taken from there.</p></dd>
<dt>pb</dt><dd><p>a logical indicating if a progress bar should be displayed</p></dd>
</dl>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='outbreaker_data.html'>outbreaker_data</a></code> to check and process data for outbreaker</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'>## see default settings</span>
<span class='fu'>create_config</span><span class='op'>(</span><span class='op'>)</span>
</div><div class='output co'>#>
#>
#> ///// outbreaker settings ///
#>
#> class: outbreaker_config list
#> number of items: 37
#>
#> /// initialisation //
#> init_tree init_mu init_kappa init_pi init_eps init_lambda
#> seqTrack 1e-04 1 0.9 0.5 0.05
#>
#> /// movements //
#> move_alpha move_swap_cases move_t_inf move_mu move_kappa
#> TRUE TRUE TRUE TRUE TRUE
#> move_pi move_eps move_lambda prop_alpha_move prop_t_inf_move
#> TRUE TRUE TRUE 0.25 0.2
#> sd_mu sd_pi sd_eps sd_lambda
#> 1e-04 0.1 0.1 0.05
#>
#> /// chains //
#> n_iter sample_every
#> 10000 50
#>
#> /// priors //
#> prior_mu prior_pi1 prior_pi2 prior_eps1 prior_eps2
#> 1 10 1 1 1
#> prior_lambda1 prior_lambda2
#> 1 1
#>
#> /// imported cases //
#> find_import n_iter_import sample_every_import outlier_threshold
#> TRUE 5000 50 5
#>
#> /// other settings //
#> paranoid min_date max_kappa ctd_directed pb
#> FALSE -10 5 FALSE FALSE </div><div class='input'>
<span class='co'>## change defaults</span>
<span class='fu'>create_config</span><span class='op'>(</span>move_alpha <span class='op'>=</span> <span class='cn'>FALSE</span>, n_iter <span class='op'>=</span> <span class='fl'>2e5</span>, sample_every <span class='op'>=</span> <span class='fl'>1000</span><span class='op'>)</span>
</div><div class='output co'>#>
#>
#> ///// outbreaker settings ///
#>
#> class: outbreaker_config list
#> number of items: 37
#>
#> /// initialisation //
#> init_tree init_mu init_kappa init_pi init_eps init_lambda
#> seqTrack 1e-04 1 0.9 0.5 0.05
#>
#> /// movements //
#> move_alpha move_swap_cases move_t_inf move_mu move_kappa
#> FALSE TRUE TRUE TRUE TRUE
#> move_pi move_eps move_lambda prop_alpha_move prop_t_inf_move
#> TRUE TRUE TRUE 0.25 0.2
#> sd_mu sd_pi sd_eps sd_lambda
#> 1e-04 0.1 0.1 0.05
#>
#> /// chains //
#> n_iter sample_every
#> 2e+05 1000
#>
#> /// priors //
#> prior_mu prior_pi1 prior_pi2 prior_eps1 prior_eps2
#> 1 10 1 1 1
#> prior_lambda1 prior_lambda2
#> 1 1
#>
#> /// imported cases //
#> find_import n_iter_import sample_every_import outlier_threshold
#> TRUE 5000 50 5
#>
#> /// other settings //
#> paranoid min_date max_kappa ctd_directed pb
#> FALSE -10 5 FALSE FALSE </div><div class='input'>
</div></pre>
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