#' outbreaker2: a platform for disease outbreak reconstruction

#'

#' 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

#'

#' 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}.

#'

#' @name outbreaker_package

#'

#' @importFrom utils packageDescription

#'

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