Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)<doi:10.1093/molbev/msm088> and plot timescaled phylogenies from any Bayesian divergence time analysis. Most timecalibrated node prior distributions require userspecified 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. Timescaled phylogenetic plots can be visualised with absolute and geological timescales . All plotting functions are applicable with output from any Bayesian software, not just 'MCMCtree'.
Package details 


Author  Mark Puttick [aut,cre], Pascal Title [ctb] 
Maintainer  Mark Puttick <[email protected]> 
License  GPL (>= 2) 
Version  1.1 
Package repository  View on CRAN 
Installation 
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