pre_clustering

This function updates the clusters and the initial tree in the lists data 
and config

Bayesian reconstruction of who infected whom during past outbreaks using routinely-collected surveillance data. Inference of transmission trees using genotype, age specific social contacts, distance between cases and onset dates of the reported cases. (Robert A, Kucharski AJ, Gastanaduy PA, Paul P, Funk S. (2020) <doi:10.1098/rsif.2020.0084>).

Alexis Robert

o2geosocial

Reconstruction of Transmission Chains from Surveillance Data

Sebastian Funk

Adam J Kucharski

Thibaut Jombart

pre_clustering function

<dl><dt>data</dt>
<dd>A list of data items as returned by <code>outbreaker_data</code>, or
arguments passed to this function.</dd>
<dt>config</dt>
<dd>A list of settings as returned by <code>create_config</code>, or
arguments passed to this function.</dd></dl>

Arguments

Alexis Robert (<a href="/link/alexis.robert%40lshtm.ac.uk?package=o2geosocial&version=1.1.2" data-mini-rdoc="o2geosocial::alexis.robert@lshtm.ac.uk">alexis.robert@lshtm.ac.uk</a>)

Author

Pre cluster cases in groups according using the genotypes and the arbitrary
thresholds gamma (spatial) and delta (temporal). — pre_clustering

<dl>

<dt>data</dt>
<dd>A list of data items as returned by <code>outbreaker_data</code>, or
arguments passed to this function.</dd>


<dt>config</dt>
<dd>A list of settings as returned by <code>create_config</code>, or
arguments passed to this function.</dd>

</dl>

Alexis Robert (<a href='mailto:alexis.robert@lshtm.ac.uk'>alexis.robert@lshtm.ac.uk</a>)

pre_clustering: Pre cluster cases in groups according using the genotypes and the arbitrary thresholds gamma (spatial) and delta (temporal).

Description

Usage

Value

Arguments

Author