PyMsBayes Documentation

Contents:

• 1. Overview
• 2. Prerequisites
  • 2.1. Optional additions
• 3. Installation
  • 3.1. Troubleshooting
• 4. PyMsBayes Tutorials
  • 4.1. Background
  • 4.2. The Configuration File
  • 4.3. Selecting Priors
  • 4.4. Getting the exampe data
  • 4.5. A Simple Empirical Analysis
  • 4.6. An Empirical Analysis under Multiple Models
  • 4.7. A Simulation-based Validation Analysis
  • 4.8. A key to the output of model parameters and associated statstics
• 5. Caveats and Recommendations
  • 5.1. Be skeptical of strongly supported results
  • 5.2. Issues of ABC model choice
  • 5.3. Assess the sensitivity of results to prior assumptions
  • 5.4. Simulation-based analyses can illuminate temporal resolution
  • 5.5. Do not scramble the summary statistics among taxa!
  • 5.6. The method might be inappropriate for comparing many taxa
  • 5.7. Please choose your priors
• 6. PyMsBayes Change History
  • 6.1. Version 0.3.5
  • 6.2. Version 0.3.4
  • 6.3. Version 0.3.3
  • 6.4. Version 0.3.2
  • 6.5. Version 0.3.1
  • 6.6. Version 0.3.0
  • 6.7. Version 0.2.2
  • 6.8. Version 0.2.1
  • 6.9. Version 0.2.0
• 7. Acknowledgements
• 8. User’s Group
• 9. Copyright and License
• 10. Citing PyMsBayes
• 11. Literature Cited

Indices and tables

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