Man pages for xavierdidelot/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... |
| BactDating | BactDating: Bayesian inference of ancestral dates on... |
| clusteredTest | Experimental clustered permutation test |
| coalpriorR | Coalescent prior function |
| collapse.singles.useRec | Modified collapse.singles() from package ape which deletes... |
| drop.tip.useRec | Modified drop.tip() from 'ape' package that also updates the... |
| 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... |
| nodeDates | Compute dates of internal nodes for a given tree |
| plotDualScale | Plot tree rescaled using dual scale |
| plot.resBactDating | Plotting methods |
| 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 |
