Stay-at-Home RevBayes Workshop Spring 2021

Location: Online Only Event (for Asia-Pacific Time Zones)
Dates: 4/21, 2021 to 6/5, 2021
Instructors: Joëlle Barido-Sottani, Walker Pett, Josh Justison, Wade Dismukes, Luiza Fabreti, Rui Borges, Ben Redelings, Mike May, April Wright, Rachel Warnock, Carrie Tribble, Paul Lewis, Michael Landis, Tracy Heath, Sebastian Höhna

Description

This free online-only RevBayes workshop will provide an introduction to the theory and use of RevBayes, with a focus on (1) tree inference from molecular data, (2) analyses combining fossil and extant taxa, and (3) evaluating MCMC performance, with advanced topics including polymorphism-aware inference, assessing model adequacy, and macroevolutionary analyses. Additional topics may be added depending on the interests of selected participants. The format will be a combination of interactive video sessions (via Zoom), real-time discussions over Slack, self-guided tutorials, and pre-recorded videos.

The initial session will resolve technical issues and present the basics of using RevBayes. Participants will then be expected to work through several tutorials on their own schedule, with the help of pre-recorded materials. A Slack forum will be open for questions and issues. The workshop will conclude with group online Q&A sessions and a 1-on-1 meeting for each participant with a course instructor. The dates for the interactive sessions are currently tentative and may be adjusted depending on the schedules of the participants and instructors.

We are hoping to identify up to 20-25 participants for this online course. We will target applicants from the Asia-Pacific regions (timezones UTC+4 to UTC+14, including UTC-10 and UTC-11). Participants will not be charged for the course, but we will request that they commit to completing the tutorials and attending a majority of interactive sessions.

Software

Before the course starts, please install the following software on your own computer:
  • Participants will need access to a computer (Unix, Mac OSX, Windows) to complete the tutorials, as well as a web-enabled device (computer or mobile device) capable of running communication tools.
  • RevBayes v1.1.1
  • Tracer
  • FigTree
  • R (we also recommend RStudio)
  • A good text editor, such as VS Code, Sublime Text, NotePad++, Atom, BBEdit, vim, or emacs
  • For communication we will use Zoom and Slack

Pre-workshop Materials

Please review the following materials before the workshop:

Schedule

  • April 21 and 22: introductions, installation troubleshooting & basics of RevBayes
  • May 26 to June 4: Q&A sessions and 1-on-1 meetings
  • Interactive sessions will be held over Zoom and the links will be announced on Slack. To accommodate all participants and the instructors, we may have to hold separate sessions at 1h-4h UTC and 13h-16h UTC (we may record some sessions and make those available to the workshop participants).
  • Tutorials

    1. Introduction to MCMC using RevBayes
    2. Nucleotide substitution models
    3. Partitioned data analysis
    4. Estimating a Time-Calibrated Phylogeny of Fossil and Extant Taxa using Morphological Data
    5. Bayesian polymorphism-aware phylogenetic inference (tutorial coming soon)
    6. Convergence assessment
    7. Introduction to Posterior Prediction
    8. Additional tutorials (optional)

    Videos

    1. RevBayes Intro to MCMC
    2. RevBayes Substitution Models
    3. RevBayes Partitioned Data Analysis
    4. RevBayes FBD Tutorial
    5. RevBayes Convergence Assessment
    6. RevBayes Intro to Posterior Prediction
    7. History of Phylogenetic Comparative Methods
    8. RevBayes BiSSE Tutorial

    Workshop Code of Conduct

    All attendees and instructors will have to agree to the terms outlined in the workshop code of conduct.

    The code of conduct for the previous edition of the workshop can be found here.