tbea

Overview

An R package for pre- and post-processing in phylogenetic and divergence-times Bayesian inference. Functions are provided for prior specification in divergence time estimation using fossils as well as other kinds of data. It provides tools for interacting with the input and output of Bayesian platforms in evolutionary biology such as ‘BEAST2’, ‘MrBayes’, ‘RevBayes’, or ‘MCMCTree’. It Implements a simple measure similarity between probability density functions for comparing prior and posterior Bayesian densities, as well as code for calculating the combination of distributions using conflation of Hill (2008). Functions for estimating the origination time in collections of distributions using the x-intercept (e.g., Draper and Smith, 1998) and stratigraphic intervals (Marshall 2010) are also available.

Hill, T. 2008. “Conflations of probability distributions”. Transactions of the American Mathematical Society, 363:3351-3372. doi:10.48550/arXiv.0808.1808

Draper, N. R. and Smith, H. 1998. “Applied Regression Analysis”. 1–706. Wiley Interscience, New York. DOI:10.1002/9781118625590,

Marshall, C. R. 2010. “Using confidence intervals to quantify the uncertainty in the end-points of stratigraphic ranges”. Quantitative Methods in Paleobiology, 291–316. DOI:10.1017/S1089332600001911.

Installation

You can now install the stable version from CRAN, and the development one using remotes:

install.packages("tbea")
remotes::install_github("gaballench/tbea")

Authorship and citation

This package was created and maintained by Gustavo A. Ballen (@gaballench) and Sandra Reinales (@spreinalesl).

Please cite this package as follows:

Ballen, G.A. & Reinales, S. (2024). tbea: tools for pre- and post-processing in Bayesian evolutionary analyses. BioRxiv https://www.biorxiv.org/content/10.1101/2024.06.18.599561.

If you use bibtex, use the following entry in your .bib file:

@article {Ballen2024.06.18.599561,
    author = {Ballen, Gustavo A. and Reinales, Sandra},
    title = {tbea: tools for pre- and post-processing in Bayesian evolutionary analyses},
    year = {2024},
    doi = {10.1101/2024.06.18.599561},
    eprint = {https://www.biorxiv.org/content/early/2024/06/19/2024.06.18.599561.full.pdf},
    journal = {bioRxiv}
}

Problems?

If you find a bug or unexpected behavior, please file an issue.