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\name{outbreaker_package}

\alias{outbreaker_package}

\title{outbreaker2: a platform for disease outbreak reconstruction}

\description{

This package provides a statistical platform for reconstructing transmission

trees ('who infects whom') in densely sampled disease outbreaks. It

reimplements, as a particular case, the model of 'outbreaker' (see

references). 'outbreaker2' extends and replaces 'outbreaker'. \cr

}

\details{

The emphasis of 'outbreaker2' is on modularity, which enables customisation

of priors, likelihoods and even movements of parameters and augmented data by

the user. This the dedicated vignette on this topic

\code{vignette("outbreaker2_custom")}.\cr

The main functions of the package are:

\itemize{

\item \code{\link{outbreaker}}: main function to run analyses

\item \code{\link{outbreaker_data}}: function to process input data

\item \code{\link{create_config}}: function to create default and customise

configuration settings

\item \code{\link{custom_priors}}: function to specify customised prior

functions

\item \code{\link{custom_likelihoods}}: function to specify customised likelihoods

functions

\item \code{\link{custom_moves}}: function to create default and customise movement

functions

}

}

\author{

Thibaut Jombart \email{thibautjombart@gmail.com}

}