tbea: Pre- And Post-Processing in Bayesian Evolutionary Analyses

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>.

Version:	1.5.0
Depends:	R (≥ 3.5.0)
Imports:	ape, Rfit, boot, graphics, stats, utils, coda
Suggests:	testthat (≥ 3.0.0), knitr, rmarkdown
Published:	2024-07-01
DOI:	10.32614/CRAN.package.tbea
Author:	Gustavo A. Ballen [aut, cre], Sandra Reinales [aut]
Maintainer:	Gustavo A. Ballen <gustavo.a.ballen at gmail.com>
BugReports:	https://github.com/gaballench/tbea/issues
License:	GPL-3
URL:	https://github.com/gaballench/tbea
NeedsCompilation:	no
Materials:	README
In views:	Phylogenetics
CRAN checks:	tbea results

Documentation:

Reference manual:	tbea.pdf
Vignettes:	Intro to tbea Choosing init vals for findParams

Downloads:

Package source:	tbea_1.5.0.tar.gz
Windows binaries:	r-devel: tbea_1.5.0.zip, r-release: tbea_1.5.0.zip, r-oldrel: tbea_1.5.0.zip
macOS binaries:	r-release (arm64): tbea_1.5.0.tgz, r-oldrel (arm64): tbea_1.5.0.tgz, r-release (x86_64): tbea_1.5.0.tgz, r-oldrel (x86_64): tbea_1.5.0.tgz
Old sources:	tbea archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=tbea to link to this page.