MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

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 either using node bars, using branch widths proportional to the age uncertainty, or by plotting the full posterior distributions on nodes. The package also gives options to include the geological timescale and other details alongside the plotted phylogeny. All plotting functions these are applicable with output from any Bayesian software, not just 'MCMCtree'.

Version: 0.1
Depends: R (≥ 3.3), ape (≥ 3.0-7), sn, coda
Imports: methods, utils, stats, grDevices, graphics
Suggests: knitr
Published: 2019-03-24
Author: Mark Puttick [aut,cre]
Maintainer: Mark Puttick <mark.puttick at bristol.ac.uk>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
CRAN checks: MCMCtreeR results

Downloads:

Reference manual: MCMCtreeR.pdf
Package source: MCMCtreeR_0.1.tar.gz
Windows binaries: r-devel: MCMCtreeR_0.1.zip, r-release: MCMCtreeR_0.1.zip, r-oldrel: MCMCtreeR_0.1.zip
OS X binaries: r-release: MCMCtreeR_0.1.tgz, r-oldrel: MCMCtreeR_0.1.tgz

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