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RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes

View ORCID ProfileCarrie M. Tribble, William A. Freyman, Michael J. Landis, Jun Ying Lim, Joëlle Barido-Sottani, Bjørn Tore Kopperud, Sebastian Höhna, Michael R. May
doi: https://doi.org/10.1101/2021.05.10.443470
Carrie M. Tribble
1Department of Integrative Biology University of California, Berkeley, CA 94709, USA
2University Herbarium, University of California, Berkeley, CA 94709, USA
3School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, 96822, USA
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  • ORCID record for Carrie M. Tribble
  • For correspondence: ctribble09@gmail.com
William A. Freyman
423andMe, Inc., Sunnyvale, CA, 94086, USA
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Michael J. Landis
5Department of Biology, Washington University in St. Louis, MO 63130, USA
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Jun Ying Lim
6School of Biological Sciences, Nanyang Technological University, Singapore 639798
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Joëlle Barido-Sottani
7Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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Bjørn Tore Kopperud
8GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
9Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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Sebastian Höhna
8GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
9Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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Michael R. May
1Department of Integrative Biology University of California, Berkeley, CA 94709, USA
2University Herbarium, University of California, Berkeley, CA 94709, USA
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Summary

  1. Statistical phylogenetic methods are the foundation for a wide range of evolutionary and epidemiological studies. However, as these methods grow increasingly complex, users often encounter significant challenges with summarizing, visualizing, and communicating their key results.

  2. We present RevGadgets, an R package for creating publication-quality figures from the results of a large variety of phylogenetic analyses performed in RevBayes (and other phylogenetic software packages).

  3. We demonstrate how to use RevGadgets through a set of vignettes that cover the most common use cases that researchers will encounter.

  4. RevGadgets is an open-source, extensible package that will continue to evolve in parallel with RevBayes, helping researchers to make sense of and communicate the results of a diverse array of analyses.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/cmt2/RevGadgets

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 11, 2021.
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RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes
Carrie M. Tribble, William A. Freyman, Michael J. Landis, Jun Ying Lim, Joëlle Barido-Sottani, Bjørn Tore Kopperud, Sebastian Höhna, Michael R. May
bioRxiv 2021.05.10.443470; doi: https://doi.org/10.1101/2021.05.10.443470
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RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes
Carrie M. Tribble, William A. Freyman, Michael J. Landis, Jun Ying Lim, Joëlle Barido-Sottani, Bjørn Tore Kopperud, Sebastian Höhna, Michael R. May
bioRxiv 2021.05.10.443470; doi: https://doi.org/10.1101/2021.05.10.443470

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