BactDating              BactDating: Bayesian inference of ancestral
                        dates on bacterial phylogenetic trees
allDates                Compute dates of leaves and internal nodes for
                        a given tree
bactdate                Main function
coalpriorR              Coalescent prior function
dualScale               Rescaling function using dual scale
initRoot                Initial tree rooting based on best root-to-tip
                        correlation
leafDates               Compute dates of leaves for a given tree
likelihoodGamma         Gamma likelihood function
likelihoodNegbin        Negative-binomial likelihood function
likelihoodPoisson       Poisson likelihood function
likelihoodRelaxedgamma
                        Relaxed gamma likelihood function
loadCFML                Load output from ClonalFrameML
loadGubbins             Load output from Gubbins
modelcompare            Perform Bayesian comparison between two models
                        based on DIC values
nodeDates               Compute dates of internal nodes for a given
                        tree
plot.resBactDating      Plotting methods
plotDualScale           Plot tree rescaled using dual scale
print.resBactDating     Print function for resBactDating objects
roottotip               Root to tip correlation
simcoaltree             Simulation of coalescent dated tree
simdatedtree            Simulation of dated tree using rtree and rexp
                        branch lengths
simobsphy               Simulation of observed phylogeny given a dated
                        tree
staph                   Data on Staphylococcus aureus ST239 from Harris
                        et al (2010)
summary.resBactDating   Summary function for resBactDating objects
