BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

Documentation for package ‘BactDating’ version 1.0

allDates	Compute dates of leaves and internal nodes for a given tree
bactdate	Main function
BactDating	BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees
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