--- a
+++ b/man/outbreaker.Rd
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/outbreaker.R
+\name{outbreaker}
+\alias{outbreaker}
+\title{outbreaker2: main function for reconstructing disease outbreaks}
+\usage{
+outbreaker(
+  data = outbreaker_data(),
+  config = create_config(),
+  priors = custom_priors(),
+  likelihoods = custom_likelihoods(),
+  moves = custom_moves()
+)
+}
+\arguments{
+\item{data}{a list of named items containing input data as returned by
+\code{\link{outbreaker_data}}}
+
+\item{config}{a set of settings as returned by \code{\link{create_config}}}
+
+\item{priors}{a set of log-prior functions as returned by
+\code{\link{custom_priors}}}
+
+\item{likelihoods}{a set of log-likelihood functions as returned by
+\code{\link{custom_likelihoods}}}
+
+\item{moves}{a set of movement functions as returned by
+\code{\link{custom_moves}}}
+}
+\description{
+The function \code{outbreaker} is the main function of the package. It runs
+processes various inputs (data, configuration settings, custom priors,
+likelihoods and movement functions) and explores the space of plausible
+transmission trees of a densely sampled outbreaks.\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
+}
+\examples{
+
+## get data
+data(fake_outbreak)
+dat <- fake_outbreak
+
+\dontrun{
+## run outbreaker
+out <- outbreaker(data = list(dna = dat$dna, dates = dat$onset, w_dens = dat$w),
+config = list(n_iter = 2e4, sample_every = 200))
+plot(out)
+as.data.frame(out)
+
+## run outbreaker, no DNA sequences
+out2 <- outbreaker(data = list(dates = dat$onset, w_dens = w),
+config = list(n_iter = 2e4, sample_every = 200))
+plot(out2)
+as.data.frame(out2)
+
+}
+}
+\references{
+Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson
+    N (2014).  Bayesian reconstruction of disease outbreaks by combining
+    epidemiologic and genomic data. PLoS Computational Biology.
+}
+\seealso{
+\code{\link{outbreaker_data}} to process input data, and
+    \code{\link{create_config}} to process/set up parameters
+
+\itemize{
+
+\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})
+}