title: RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses.
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.
authors.affiliation: Department of Biological Sciences, Macquarie University, Sydney, Australia.
authors.forename: Dan L
authors.initials: DL
authors.lastname: Warren
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Geneva
authors.affiliation: Department of Biological Sciences, Macquarie University, Sydney, Australia.|Division of Evolution, Ecology, and Genetics, Australian National University, Canberra, Australia.
authors.forename: Robert
authors.initials: R
authors.lastname: Lanfear
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D010802:Phylogeny; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: MCMC; convergence; phylogenetics; stationarity; topology