MCMCtreeR

Provides functions to prepare time priors for 'MCMCtree' analyses in the 'PAML' software from Yang (2007)[https://doi.org/10.1093%2Fmolbev%2Fmsm088] 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'.

Last 30 days

This package has been downloaded 193 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 3 times.

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Last 365 days

This package has been downloaded 2,560 times in the last 365 days. That's enough downloads to impress a room full of undergrads. A commendable achievement indeed. The day with the most downloads was Jul 21, 2024 with 74 downloads.

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