get.Rt                  Derive reproduction numbers from outbreak's
                        outputs
get.mu                  Derive mutation rate estimation from outbreak's
                        outputs
get.tTree               Simple transmission tree from outreaber's
                        output
outbreaker              Outbreaker: disease outbreak reconstruction
                        using genetic data
outbreaker.package      outbreaker: disease outbreak reconstruction
                        using epidemiological and genetic data
plotChains              Plot outbreaker's results
selectChains            Select 'good' runs from independent MCMC chains
simOutbreak             Simulation of pathogen genotypes during disease
                        outbreaks
simulated outbreak dataset
                        Toy outbreak dataset used to illustrate
                        outbreaker
