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 1.1.0

- DESCRIPTION file.

## Help Pages

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