BactDating              BactDating: Bayesian inference of ancestral
                        dates on bacterial phylogenetic trees
allDates                Compute dates of leaves and internal nodes for
                        a given tree
as.mcmc.resBactDating   Convert to coda mcmc format
as.treedata.resBactDating
                        Convert to treedata format from ggtree package
bactdate                Main function of BactDating package to date the
                        nodes of a phylogenetic tree
clusteredTest           Experimental clustered permutation test
coalpriorR              Coalescent prior function
collapse.singles.useRec
                        Modified collapse.singles() from package ape
                        which deletes the single nodes (i.e., with a
                        single descendant) in a tree, respecting the
                        rec function. Internal, used by drop.tip.rec
drop.tip.useRec         Modified drop.tip() from 'ape' package that
                        also updates the recombination proportions
                        added when loaded from CFML or Gubbins
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
likelihoodArc           arc likelihood function
likelihoodCarc          carc likelihood function
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
