--- a
+++ b/man/outbreaker_package.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/package.R
+\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}
+}