R: BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

# BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

## Documentation for package ‘BactDating’ version 1.0

- DESCRIPTION file.

## Help Pages

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