Olivier Gimenez

Bayesian Analysis of Capture-Recapture Data with Hidden Markov Models: Theory and Case Studies in R and NIMBLE introduces ecologists and statisticians to a powerful and unifying framework for analysing capture-recapture data. Hidden Markov models (HMMs) have become a cornerstone in modern population ecology, offering a flexible way to decompose complex processes such as survival, recruitment, and dispersal into simpler building blocks, while explicitly accounting for the fact that we only observe imperfect data rather than the true underlying states. Combined with Bayesian inference, HMMs provide a natural and transparent approach to handle uncertainty, explore model structures, and draw robust conclusions. This book illustrates how to bring these ideas to life using the R package NIMBLE, a fast-developing environment for building and fitting hierarchical models. Key features include: • A clear introduction to the principles of Bayesian statistics, HMMs, and the NIMBLE package • Step-by-step tutorials showing how to implement a wide range of capture-recapture models for open populations • Fully reproducible examples with data and R code, following a “learning by doing” philosophy • Case studies drawn from the ecological literature, illustrating how to apply methods to real-world conservation questions • Practical guidance on model specification, coding strategies, and interpretation of results Written in an accessible style, this book is designed for ecologists, wildlife biologists, and conservation scientists who already use R and wish to deepen their modelling toolkit, as well as statisticians interested in ecological applications. Beginners will find a self-contained path into Bayesian capture-recapture modelling, while experienced researchers will discover a flexible framework to extend and adapt to their own data and questions.

Novel Statistical Tools for Conserving and Managing PopulationsBy gathering information on key demographic parameters, scientists can often predict how populations will develop in the future and relate these parameters to external influences, such as global warming. Because of their ability to easily incorporate random effects, fit state-space models, evaluate posterior model probabilities, and deal with missing data, modern Bayesian methods have become important in this area of statistical inference and forecasting. Emphasising model choice and model averaging, Bayesian Analysis for Population Ecology presents up-to-date methods for analysing complex ecological data. Leaders in the statistical ecology field, the authors apply the theory to a wide range of actual case studies and illustrate the methods using WinBUGS and R. The computer programs and full details of the data sets are available on the book’s website.The first part of the book focuses on models and their corresponding likelihood functions. The authors examine classical methods of inference for estimating model parameters, including maximum-likelihood estimates of parameters using numerical optimisation algorithms. After building this foundation, the authors develop the Bayesian approach for fitting models to data. They also compare Bayesian and traditional approaches to model fitting and inference.Exploring challenging problems in population ecology, this book shows how to use the latest Bayesian methods to analyse data. It enables readers to apply the methods to their own problems with confidence.

The study of ecological systems is often impeded by components that escape perfect observation, such as the trajectories of moving animals or the status of plant seed banks. These hidden components can be efficiently handled with statistical modeling by using hidden variables, which are often called latent variables. Notably, the hidden variables framework enables us to model an underlying interaction structure between variables (including random effects in regression models) and perform data clustering, which are useful tools in the analysis of ecological data.This book provides an introduction to hidden variables in ecology, through recent works on statistical modeling as well as on estimation in models with latent variables. All models are illustrated with ecological examples involving different types of latent variables at different scales of organization, from individuals to ecosystems. Readers have access to the data and R codes to facilitate understanding of the model and to adapt inference tools to their own data.

Novel Statistical Tools for Conserving and Managing PopulationsBy gathering information on key demographic parameters, scientists can often predict how populations will develop in the future and relate these parameters to external influences, such as global warming. Because of their ability to easily incorporate random effects, fit state-space models, evaluate posterior model probabilities, and deal with missing data, modern Bayesian methods have become important in this area of statistical inference and forecasting. Emphasising model choice and model averaging, Bayesian Analysis for Population Ecology presents up-to-date methods for analysing complex ecological data. Leaders in the statistical ecology field, the authors apply the theory to a wide range of actual case studies and illustrate the methods using WinBUGS and R. The computer programs and full details of the data sets are available on the book’s website.The first part of the book focuses on models and their corresponding likelihood functions. The authors examine classical methods of inference for estimating model parameters, including maximum-likelihood estimates of parameters using numerical optimisation algorithms. After building this foundation, the authors develop the Bayesian approach for fitting models to data. They also compare Bayesian and traditional approaches to model fitting and inference.Exploring challenging problems in population ecology, this book shows how to use the latest Bayesian methods to analyse data. It enables readers to apply the methods to their own problems with confidence.