Workshop at NIMBioS - Knoxville, TN USA
- Sebastian Höhna (lead organizer)
- Bastien Boussau
- Emma Goldberg
- Tracy Heath
- John Huelsenbeck
- Will Freyman
To prepare for the workshop, please see detailed information: https://revbayes.github.io/RevBayes-NIMBioS-Workshop/workshop-prep
Detailed schedule timeline: link
Repository for slides: https://github.com/revbayes/RevBayes-NIMBioS-Workshop/tree/master/slides
Topics
- Introduction/Overview
- Probability, Bayesian Statistics, MCMC
- Likelihood based phylogenetics [slides]
- Introduction to RevBayes [slides]
Practical: Introduction to RevBayes
- Tutorial PDF: RB_MCMC_Intro_Tutorial.pdf
Practical: Models of Molecular Evolution
- Tutorial PDF: RB_CTMC_Tutorial.pdf
- Primates data
- JC Rev script
- GTR+I+G Rev script
Topics
Practical: Model Selection
- Tutorial PDF: RB_BayesFactor_Tutorial.pdf
- Data file
- Rev script
Practical: Partition Models
- Tutorial PDF: RB_Partition_Tutorial.pdf
- Data files
- Rev scripts
Practical: Model Fit
- Tutorial PDF: RB_PosteriorPrediction_Tutorial.pdf
- Data files
- Rev scripts
Practical: MCMC & Convergence
- Tutorial PDF: RB_MCMC_Tutorial.pdf
- Rev scripts
Topics
- Divergence-time estimation [slides]
- Clock Models
- Node Calibration
- Total Evidence Analysis
Practical: Clock Models
- Tutorial PDF: RB_ClockModels_Tutorial.pdf
- Data file
- Tree file
- Rev scripts
Practical: Total Evidence Analysis under the Fossilized Birth-Death Process
- Tutorial PDF: RB_TotalEvidenceDating_FBD_Tutorial.pdf
- Data files
- Rev scripts
Topics
- Estimating Diversification Rates Through-Time
- Lineage-Specific Diversification Rates
- Character State-Dependent Diversification Rates
- Biogeography
- [slides for second two topics]
Practical: Basic diversification using constant-rate birth-death models
- Tutorial PDF: RB_DiversificationRate_Tutorial.pdf
- Data files
- Rev scripts
Practical: Diversification rates through time using episodic birth-death models
Practical: Branch-specific diversification rate estimation
Practical: Character state-dependent diversification
- Tutorial PDF: RB_DiversificationRate_CharacterDependent_Tutorial.pdf
- Data files
- Rev scripts
- RevGadgets R package
Practical: Biogeography
- Tutorial PDF: RB_Biogeography_Tutorial.pdf
- Data files
- Rev scripts
- Also, the second part of the Biogeography Practical uses the Character state-dependent diversification materials above.
Topics
-
Gene-tree/species-tree estimation
-
The multispecies coalescent model
-
[slides]
-
Tutorial PDF: RB_MultispeciesCoalescent_Tutorial.pdf