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

Research output: Contribution to journalArticle

71 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 languageEnglish (US)
Pages (from-to)1016-1020
Number of pages5
JournalMolecular Biology and Evolution
Volume34
Issue number4
DOIs
StatePublished - Apr 1 2017

Keywords

  • Convergence
  • MCMC
  • MCMC
  • Phylogenetics
  • Stationarity
  • Topology

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

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