BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

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Documentation for package ‘BactDating’ version 1.1.0

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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