--- a +++ b/R/package.R @@ -0,0 +1,41 @@ +#' 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 +#' +NULL