RevBayes Demonstration and Mini Workshop

Location: Montana State University, Bozeman, MT USA
Dates: 4/12, 2018
Instructors: Tracy Heath

Description

This workshop will introduce RevBayes and the Rev language. We will focus on the basics of the software and hierarchical Bayesian modeling. We will work together through one tutorial. I will walk through setting up a phylogenetic analysis of fossil and molecular data. Then we will discuss the other models and methods available in RevBayes.

Date Time Topic Material Instructors
Tuesday 09:30-10:30 Lecture: Hierarchical Bayesian Modeling for Phylogenetic Inference using RevBayes Lecture slides 👩🏻‍🏫
Tuesday 10:30-11:00 Morning Tea
Tuesday 11:00-12:00 Lecture: Introduction to Bayesian Inference and MCMC in RevBayes Lecture slides 👩🏻‍🏫
Tuesday 12:00-13:30 Lunch 🥪
Tuesday 13:30-14:00 Resources for using RevBayes https://revbayes.com 👩🏻‍🏫
Tuesday 14:00-15:30 Lab: Phylogenetic Inference using RevBayes Nucleotide substitution models 💻
Tuesday 15:30-16:00 Afternoon Tea 🍵
Tuesday 16:00-17:30 Lab: Phylogenetic Inference using RevBayes, continued 💻
Wednesday 09:30-10:30 Lecture: Bayesian Divergence-Time Estimation Lecture slides 👩🏻‍🏫
Wednesday 10:30-11:00 Morning Tea
Wednesday 11:30-12:30 Lecture: Bayesian Divergence-Time Estimation, continued 👩🏻‍🏫
Wednesday 12:30-14:00 Lunch 🍜
Wednesday 14:00-15:30 Lab: Estimating Trees and Divergence Times Combined-Evidence Analysis and the Fossilized Birth-Death Process for Analysis of Fossil and Extant Specimens 💻
Wednesday 15:30-16:00 Afternoon Tea 🍵
Wednesday 16:00-17:30 Lab: Estimating Trees and Divergence Times, continued 💻
Thursday 09:30-10:30 Lab: Historical Biogeography Simple Phylogenetic Analysis of Historical Biogeography 💻
Thursday 10:30-11:00 Morning Tea
Thursday 11:00-12:30 Lab: Modeling Branch-Heterogeneous Processes 💻
Thursday 12:30-14:00 Lunch 🍔
Thursday 14:00-15:30 Presentations by ANU Researchers 🇦🇺
Thursday 15:30-16:00 Afternoon Tea 🍵
Thursday 16:00-15:30 Discussion and Open Lab 🗣
Sunday 08:00-08:45 Intro to Bayesian inference Bayesian slides
MCMC slides
Rosana Zenil-Ferguson
Sunday 08:45-09:00 Break
Sunday 09:00-11:00 Intro to graphical models and RevBayes Introduction to Graphical Models Will Freyman
Sunday 11:00-11:15 Break
Sunday 11:15-12:00 Phylogenetic tree inference CTMC slides Rosana Zenil-Ferguson
Sunday 12:00-01:00 Lunch
Sunday 01:00-03:00 Phylogenetic tree inference in RevBayes Nucleotide substitution models Will Freyman
Sunday 03:00-03:10 Break
Sunday 03:10-03:40 Models linking trait evolution to diversification Diversification slides Rosana Zenil-Ferguson
Sunday 03:40-05:00 State-dependent speciation and extinction models State-dependent diversification with BiSSE and MuSSE Will Freyman
Tuesday 09:00-09:30 Welcome to the Workshop Sebastian Höhna
Tuesday 09:30-10:15 RevBayes Introduction Sebastian Höhna
Tuesday 10:15-10:30 Coffee break
Tuesday 10:30-12:00 Substitution Models in Phylogenetics Sebastian Höhna
Tuesday 12:00-13:00 Lunch break
Tuesday 13:00-15:00 Practical on inferring phylogenies (Part I) Nucleotide substitution models Sebastian Höhna
Tuesday 15:00-15:15 Coffee break
Tuesday 15:15-17:30 Practical on inferring phylogenies (Part II) Nucleotide substitution models Sebastian Höhna
Wednesday 09:00-09:30 Recap MCMC and Substitution Models Sebastian Höhna
Wednesday 09:30-10:15 Morphological models Joe O'Reilley, Mark Puttick
Wednesday 10:15-10:30 Coffee break
Wednesday 10:30-12:00 Divergence time estimation using the fossilized birth-death model Walker Pett
Wednesday 12:00-13:00 Lunch break
Wednesday 13:00-15:00 Practical on divergence time estimation using the fossilized birth-death model (Part I) Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Walker Pett
Wednesday 15:00-15:15 Coffee break
Wednesday 15:15-17:30 Practical on divergence time estimation using the fossilized birth-death model (Part II) Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Walker Pett
Thursday 09:00-09:30 Recap Walker Pett
Thursday 09:30-10:15 Diversification rate estimation (Part I) Sebastian Höhna
Thursday 10:15-10:30 Coffee break
Thursday 10:30-12:00 Diversification rate estimation (Part II) Rachel Warnock
Thursday 12:00-13:00 Lunch break
Thursday 13:00-15:00 Choice of practical on diversification rate estimation (Part I)
  • Simple Diversification Rate Estimation
  • Rachel Warnock, Sebastian Höhna
    Thursday 15:00-15:15 Coffee break
    Thursday 15:15-17:30 Choice of practical on diversification rate estimation (Part II)
  • Macroevolutionary Analysis of Stratigraphic Range Data
  • Episodic Diversification Rate Estimation
  • Environmental-dependent Speciation & Extinction Rates
  • Branch-Specific Diversification Rate Estimation
  • Background on state-dependent diversification rate estimation
  • State-dependent diversification with BiSSE and MuSSE
  • Rachel Warnock, Sebastian Höhna
    Friday 09:00-10:00 Lecture: An introduction to Bayesian phylogenetics using morphology Mark Puttick
    Friday 10:10-11:00 Lecture: An introduction to graphical models and Bayesian phylogenetics using RevBayes Rachel Warnock
    Friday 11:10-12:30 Lab: Phylogenetic inference using discrete morphology using RevBayes Discrete morphology - Tree Inference Joseph O'Reilly
    Monday 09:00-09:30 Welcome to the Workshop Luis Palazzesi
    Monday 09:30-10:15 RevBayes Introduction Sebastian Höhna
    Monday 10:15-10:30 Coffee break
    Monday 10:30-12:00 Substitution Models in Phylogenetics Sebastian Höhna
    Monday 12:00-13:00 Lunch break
    Monday 13:00-15:00 Practical on inferring phylogenies (Part I) Nucleotide substitution models Sebastian Höhna, Luis Palazzesi
    Monday 15:00-15:15 Coffee break
    Monday 15:15-17:30 Practical on inferring phylogenies (Part II) Nucleotide substitution models Sebastian Höhna, Luis Palazzesi
    Tuesday 09:00-09:30 Recap MCMC and Substitution Models Sebastian Höhna
    Tuesday 09:30-10:15 Divergence time estimation Sebastian Höhna
    Tuesday 10:15-10:30 Coffee break
    Tuesday 10:30-12:00 Tip-dating and the fossilized-birth-death model Sebastian Höhna
    Tuesday 12:00-13:00 Lunch break
    Tuesday 13:00-15:00 Divergence time estimation Relaxed Clocks & Time Trees Femke Thon, Sebastian Höhna
    Tuesday 15:00-15:15 Coffee break
    Tuesday 15:15-17:30 Practical on tip-dating and the fossilized-birth-death model Combined-Evidence Analysis and the Fossilized Birth-Death Process for Stratigraphic Range Data Femke Thon, Sebastian Höhna
    Wednesday 09:00-09:30 Recap Sebastian Höhna
    Wednesday 09:30-10:15 Diversification rate estimation (Part I) Sebastian Höhna
    Wednesday 10:15-10:30 Coffee break
    Wednesday 10:30-12:00 Diversification rate estimation (Part II) Sebastian Höhna
    Wednesday 12:00-13:00 Lunch break
    Wednesday 13:00-15:00 Practical on diversification rate estimation (Part I) Simple Diversification Rate Estimation Luis Palazzesi, Femke Thon, Sebastian Höhna
    Wednesday 15:00-15:15 Coffee break
    Wednesday 15:15-17:30 Practical on diversification rate estimation (Part II) Branch-Specific Diversification Rate Estimation Luis Palazzesi, Femke Thon, Sebastian Höhna
    Friday 09:00-10:00 Lecture: An Introduction to Bayesian Phylogenetics using RevBayes Tracy Heath
    Friday 10:00-11:00 Lab: Basic MCMC Introduction to MCMC using RevBayes Tracy Heath
    Friday 11:00-12:00 Lab: Phylogenetic Inference in RevBayes Nucleotide substitution models Tracy Heath

    Tutorials

    Additional Information

    Please be sure to download and install RevBayes. Go to the Software page for more information.

    Slides

    Here are some lecture slides that are similar to the ones presented in the workshop. These slides cover the basics of phylogenetic inference and analysis using RevBayes.

    Introduction to Bayesian Phylogenetics from Tracy Heath
    Bayesian Divergence Time Estimation – Workshop Lecture from Tracy Heath