RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses

Dan L. Warren; Anthony J. Geneva; Robert Lanfear; Michael Rosenberg

doi:10.1093/molbev/msw279

RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses

Dan L. Warren, Anthony J. Geneva, Robert Lanfear, Michael Rosenberg

CLAS-NS: Life Sciences, School of (SOLS)

Research output: Contribution to journal › Article › peer-review

85 Scopus citations

Abstract

Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.

Original language	English (US)
Pages (from-to)	1016-1020
Number of pages	5
Journal	Molecular biology and evolution
Volume	34
Issue number	4
DOIs	https://doi.org/10.1093/molbev/msw279
State	Published - Apr 1 2017

Keywords

Convergence
MCMC
MCMC
Phylogenetics
Stationarity
Topology

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Molecular Biology
Genetics

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10.1093/molbev/msw279

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abstract = "Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.",

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