BAMM Documentation

• 1. Introduction
  • 1.1. Bayesian Analysis of Macroevolutionary Mixtures
  • 1.2. Why Use BAMM?
• 2. Announcements
  • 2.1. June 22-23: Macroevolution / diversification short course
• 3. BAMM graph gallery
  • 3.1. Phylorate plot
  • 3.2. Individual rate-shift configurations sampled by BAMM
  • 3.3. Distinct shift configurations and their frequencies
  • 3.4. Macroevolutionary cohort matrix
  • 3.5. Phenotypic evolutionary rates
  • 3.6. Rate variation through time: color density plot
  • 3.7. Evolutionary rate variation through time: grayscale
• 4. Rate Shifts on Phylogenies: Theoretical Background
  • 4.1. The BAMM model is an approximation
  • 4.2. Multiple distinct rate shift configurations can explain your data
  • 4.3. Rate shifts are not independent
  • 4.4. Analysis of rate shifts in the BAMM framework
  • 4.5. Appendix
• 5. Quick-start guide to BAMM
  • 5.1. Control file
  • 5.2. Speciation-extinction analyses
  • 5.3. Phenotypic evolution
  • 5.4. BAMM output: brief
• 6. Setting Up BAMM
  • 6.1. Check your BAMM version
  • 6.2. Installation from Homebrew (OS X only)
  • 6.3. Installation from Executable
  • 6.4. Installation from Source
  • 6.5. Running
• 7. Configuration
  • 7.1. Control File
  • 7.2. General Options and Parameters
  • 7.3. Speciation/Extinction Model
  • 7.4. Phenotypic Evolution Model
• 8. Analyzing BAMM output with BAMMtools
  • 8.1. Brief
  • 8.2. BAMMtools quickstart guide
  • 8.3. BAMM output and the bammdata object
  • 8.4. Assessing MCMC convergence
  • 8.5. Analysis of rate shifts
  • 8.6. Bayes factors for model comparison
  • 8.7. Clade-specific evolutionary rates
  • 8.8. Branch & tip-specific evolutionary rates
  • 8.9. Rate-through-time analysis
  • 8.10. Macroevolutionary cohort analysis
  • 8.11. Cumulative shift probabilities
• 9. Advanced analysis options
  • 9.1. Accounting for non-random incomplete taxon sampling in diversification studies
  • 9.2. Priors on rate parameters
  • 9.3. Modeling less complex evolutionary scenarios
  • 9.4. Accounting for phylogenetic uncertainty
  • 9.5. Understanding the event data file
• 10. Color ramps and phylorate plots
  • 10.1. What options are available?
  • 10.2. A note of caution
  • 10.3. What should you do?
  • 10.4. How do I plot these histograms?
• 11. Frequently Asked Questions
  • 11.1. General
• 12. The BAMM likelihood function
  • 12.1. Overview
  • 12.2. Is the BAMM likelihood computed correctly?
  • 12.3. Numerical approximations in BAMM
• 13. Is BAMM reliable? A DIY approach
  • 13.1. Overview
  • 13.2. Assessing rate reliability on your own
  • 13.3. Simulating trees with rate shifts under a Poisson process
  • 13.4. Worked example: tree simulation with specified seed
  • 13.5. Worked example #1: tree with seed = 8
  • 13.6. Worked example #2: tree with seed = 9
  • 13.7. Worked example #3: tree with seed = 15
  • 13.8. General guidelines
• 14. Metropolis coupled Markov chain Monte Carlo [(MC)³]
  • 14.1. Multi-core Metropolis coupled MCMC [(MC)⁴]
  • 14.2. (MC)³ settings in BAMM
• 15. STRAPP: STructured Rate Permutations on Phylogenies
• 16. Time-flip proposal: Time-constant and time-variable shifts
  • 16.1. Calculation of parameters after a time-flip
  • 16.2. Acceptance probability for a time-flip proposal
  • 16.3. Time-flip proposal options
• 17. fossil BAMM
• 18. Troubleshooting
  • 18.1. Installation
  • 18.2. Running
  • 18.3. Analysis
• 19. Glossary

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