Function reference • BactDating

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`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
`extractSample()`	Extract a sample of trees
`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

Reference

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