README.md

Bayesian Population Analysis using WinBUGS

Models from the book "Bayesian Population Analysis using WinBUGS --- A Hierarchical Perspective" (2012) by Marc Kéry and Michael Schaub.

Original BUGS code and data files are available at the website of the book.

Stan translations was done by Hiroki Itô abies.firma@gmail.com. I thank Dr. Kéry and Dr. Schaub for permitting to publish Stan translated models. I also thank Dr. Keiichi Fukaya for helpful advice, and Dr. Bob Carpenter for reviewing the code.

Contents of the book

  • Chapter 1. Introduction
  • Chapter 2. Brief Introduction to Bayesian Statistical Modeling
  • Chapter 3. Introduction to the Generalized Linear Model: The Simplest Model for Count Data
  • Chapter 4. Introduction to Random Effects: Conventional Poisson GLMM for Count Data
  • Chapter 5. State-Space Models for Population Counts
  • Chapter 6. Estimation of the Size of a Closed Population from Capture-Recapture Data
  • Chapter 7. Estimation of Survival from Capture-Recapture Data Using the Cormack-Jolly-Seber Model
  • Chapter 8. Estimation of Survival Using Mark-Recovery Data
  • Chapter 9. Estimation of Survival and Movement from Capture-Recapture Data Using Multistate Models
  • Chapter 10. Estimation of Survival, Recruitment, and Population Size from Capture-Recapture Data Using the Jolly-Seber Model
  • Chapter 11. Estimation of Demographic Rates, Population Size, and Projection Matrices from Multiple Data Types Using Integral Population Models
  • Chapter 12. Estimation of Abundance from Counts in Metapopulation Design Using the Binomial Mixture Model
  • Chapter 13. Estimation of Occupancy and Species Distributions from Detection/Nondetection Data in Metapopulation Designs Using Site-Occupancy Models
  • Chapter 14. Concluding Remarks