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Online companion for
Marc Kéry (2010) Introduction to WinBUGS for Ecologists. Academic Press, Burlington.

A creed for models, algebra and WinBUGS
To make sense of an observation, everybody needs a model ...
whether he knows it or not.

It is difficult to imagine another method
that so effectively fosters clear thinking about a system
than the use of a model written in the language of algebra.

One of the most transparent ways
of building a model
is by describing it in the BUGS language.

Cover photo: Rosalia alpina, Switzerland, 2006 (T. Marent)

Book description

This book is a very gentle introduction for ecologists to Bayesian analysis using WinBUGS. It covers the linear model and its extensions to the generalised linear (GLM) and to the linear and generalised linear mixed models by way of extensive and fully documented examples with all code shown. All data sets are simulated in program R ; simulation allows a much greater insight into data and their analysis than the use of real data sets where truth is unknown. I believe that when you are able to simulate a data set for a particular model, then you understand that model. Indeed, one of the nicest things that somebody has said to me about my book was this: Your book made me finally understand the linear model and the GLM. You can get your copy here: www.amazon.com

For more information about the book, you can read its Preface and two sample chapters, chapter 4 and chapter 15.

Introduction to JAGS for ecologists

Development of software WinBUGS was discontinued back in 2005, but fortunately for ecologists, the BUGS language lives on in the new software JAGS, Nimble and also OpenBUGS. You can run almost all the code in the book as-is. Some changes are required only for the interface with R. The following link: Code_Kery2010_with_JAGS.R, displays a text file that contains all the R and BUGS language code from the book, which lets you run everything in JAGS, linked to R via the R package jagsUI (Kellner 2019).

Website description

This website contains additional information on the book, R, WinBUGS and JAGS code for all examples in the book as well as solutions to the exercises and bonus material. Later, there will also be a list of errors.

Table of contents

Below is a concise table of contents of the book. You can find the complete TOC here: Table of Contents
  1. Introduction
  2. Introduction to the Bayesian analysis of a statistical model
  3. WinBUGS
  4. A first session in WinBUGS: The "model of the mean"
  5. Running WinBUGS from R via R2WinBUGS
  6. Key components of (generalised) linear models: Statistical distributions and the linear predictor
  7. t-Test: Equal and unequal variances
  8. Normal linear regression
  9. Normal one-way ANOVA
  10. Normal two-way ANOVA
  11. General linear model (ANCOVA)
  12. Linear mixed-effects model
  13. Introduction to the Generalised linear model (GLM): Poisson t-test
  14. Overdispersion and offsets in the GLM
  15. Poisson ANCOVA
  16. Poisson mixed-effects model (Poisson GLMM)
  17. Binomial t-test
  18. Binomial ANCOVA
  19. Binomial mixed-effects model (Binomial GLMM)
  20. Non-standard GLMMs 1: Site-occupancy species distribution model
  21. Non-standard GLMMs 2: Binomial mixture model for the modeling of abundance
  22. Conclusions

R/WinBUGS code (for JAGS, see towards the start of the page!)

You will use WinBUGS called from R throughout the book with the exception of chapter 4, where we use WinBUGS as a standalone application for the simplest example of a linear model: the estimation of the mean of a normal population. Here, you can download that WinBUGS document ( The_model_of_the_(normal)_mean.odc)

Text file with all R/WinBUGS code: R_WB_code.txt

Solutions to exercises

There is a series of exercises at the end of most chapters; here are the solutions: Link to Solutions.txt

The Swiss hare data

This is the only real-world data set you will meet in the book. We deal with it extensively in the exercises. The Swiss hare data contain replicated counts of Brown hares (Lepus europaeus: see chapter 13) conducted over 17 years (1992-2008) at 56 sites in 8 regions of Switzerland. Replicated means that each year two counts were conducted during a two-week period. Sites vary in area, elevation, and belong to two types of habitat (arable and grassland): hence, there are both continuous and discrete explanatory variables. Unbounded counts may be modeled as Poisson random variables with log(area) as an offset, but we can also treat the observed density (i.e., the ratio of a count to area) as a normal or the incidence of a density exceeding some threshold as a binomial random variable. Hence, you can practice with all models shown in this book and meet features of genuine data sets such as missing values and other nuisances of real life.

Download text file containing the Swiss hare data.

List of errors and replies to comments

Thank you for pointing out errors to me at marc_kery@vogelwarte.ch.
I am also grateful for any comments you might have on the book.

Erratum: (None found yet ...) (Later Link to Erratum.html)

How to present the results from a Bayesian analysis

Somebody pointed out to me that there is little in my book about the way in which the results from a Bayesian analysis are presented in a paper. This may be true. I give a very brief example of this at the end of chapter 4, but in later chapters, this is not shown any longer in a very explicit manner. I may add a little document with more explanations (or examples) on that topic later, but for the moment I simply refer you to any journal article that uses Bayesian modeling. For instance, you can check out almost all of mine that are in the List of References of the book.

Information on a similar, but more advanced book published in 2012: Bayesian Population Analysis using WinBUGS by Kéry & Schaub

The current book is targeted at ecologists, but the statistical models are simply general regression models with their ordinary extensions. There are only two chapters on the kinds of models that ecologists use for more specialized inference about populations (the last two chapters). My colleague, Michael Schaub, and I I have just written a more advanced sequel to this book, which has been published by Academic Press in 2012. We call it the BPA book. It covers a fairly comprehensive selection of specialized ecological statistical models for the analysis of populations using WinBUGS, not unlike the landmark book by Royle and Dorazio (2008), but in a similar format as the current book. For more information about our new book, see its full table of contents: BPA_TOC.pdf

Workshops

Both the WinBUGS introduction and the more advanced Bayesian population analysis (BPA) book grew out of workshops that I teach (BPA together with Michael Schaub). Both workshops last about 5 days. We have taught them repeatedly in Europe and in the United States. Send me Marc an email if you're interested in hosting or attending one.

Acknowledgements

I thank Andy Royle for helping me to fledge as a statistical ecologist and BUGS programmer, Jim Nichols for teaching me how to be a scientist and for writing the foreword, Jim Hines for creating and maintaining this website, and to my family (Susana and Gabriel) for their love and their patience.

This page last revised: 27-March-2019