Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees
Estimate a Uniform Distribution for MCMCtree
Estimate Cauchy Distribution for MCMCtree
Fixed Age for MCMCtree analysis input
Estimate Gamma Distribution for MCMCtree analysis
Estimate Skew Normal for MCMCtree analysis
Estimate Skew-t Distribution for MCMCtree analysis
Estimate Upper Age for MCMCtree analysis
Plot time-scaled phylogenies
MCMCtreePhy
Add Node Constraints to Tree in MCMCtree Format
Plot distribution from MCMCtree node estimations
priorPosterior
Read MCMCtree output tree into R
Find Descendent Tips From A Common Ancestor
Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot time-scaled phylogenies from any Bayesian divergence time analysis. Most time-calibrated node prior distributions require user-specified parameters. The package provides functions to refine these parameters, so that the resulting prior distributions accurately reflect confidence in known, usually fossil, time information. These functions also enable users to visualise distributions and write 'MCMCtree' ready input files. Additionally, the package supplies flexible functions to visualise age uncertainty on a plotted tree with using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. Time-scaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.