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RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses

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dc.contributor.authorWarren, Dan L.
dc.contributor.authorGeneva, Anthony J.
dc.contributor.authorLanfear, Robert
dc.date.accessioned2021-09-14T01:45:26Z
dc.date.available2021-09-14T01:45:26Z
dc.date.issued2017
dc.date.updated2020-11-23T11:05:15Z
dc.description.abstractBayesian 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.en_AU
dc.description.sponsorshipThis work was funded in part by Australian Research Council fellowship awards to D.L.W. and R.L.en_AU
dc.format.mimetypeapplication/pdfen_AU
dc.identifier.issn0737-4038en_AU
dc.identifier.urihttp://hdl.handle.net/1885/247849
dc.language.isoen_AUen_AU
dc.provenancehttps://v2.sherpa.ac.uk/id/publication/1377..."The Published Version can be archived in a Non-Commercial Institutional Repository" from SHERPA/RoMEO site (as at 14/09/2021).en_AU
dc.publisherSociety for Molecular Biology Evolutionen_AU
dc.rights© 2017 The Author(s)The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.en_AU
dc.sourceMolecular Biology and Evolutionen_AU
dc.subjectMCMCen_AU
dc.subjectphylogeneticsen_AU
dc.subjecttopologyen_AU
dc.subjectMCMCen_AU
dc.subjectconvergenceen_AU
dc.subjectstationarityen_AU
dc.titleRWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analysesen_AU
dc.typeJournal articleen_AU
dcterms.accessRightsOpen Accessen_AU
local.bibliographicCitation.issue4en_AU
local.bibliographicCitation.lastpage1020en_AU
local.bibliographicCitation.startpage1016en_AU
local.contributor.affiliationWarren, Dan L., Macquarie Universityen_AU
local.contributor.affiliationGeneva, Anthony J., Harvard Universityen_AU
local.contributor.affiliationLanfear, Robert, College of Science, ANUen_AU
local.contributor.authoruidLanfear, Robert, u4595144en_AU
local.description.notesImported from ARIESen_AU
local.identifier.absfor060309 - Phylogeny and Comparative Analysisen_AU
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciencesen_AU
local.identifier.ariespublicationu9511635xPUB1665en_AU
local.identifier.citationvolume34en_AU
local.identifier.doi10.1093/molbev/msw279en_AU
local.identifier.scopusID2-s2.0-85018988092
local.identifier.thomsonID000396762200019
local.publisher.urlhttps://academic.oup.com/mbeen_AU
local.type.statusPublished Versionen_AU

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