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Bayesian Models

Bayesian Models

Author: N. Thompson Hobbs, Mevin B. Hooten
Publisher: Princeton University Press
ISBN: 1400866553
Pages: 320
Year: 2015-08-04
Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods—in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probability and develops a step-by-step sequence of connected ideas, including basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and inference from single and multiple models. This unique book places less emphasis on computer coding, favoring instead a concise presentation of the mathematical statistics needed to understand how and why Bayesian analysis works. It also explains how to write out properly formulated hierarchical Bayesian models and use them in computing, research papers, and proposals. This primer enables ecologists to understand the statistical principles behind Bayesian modeling and apply them to research, teaching, policy, and management. Presents the mathematical and statistical foundations of Bayesian modeling in language accessible to non-statisticians Covers basic distribution theory, network diagrams, hierarchical models, Markov chain Monte Carlo, and more Deemphasizes computer coding in favor of basic principles Explains how to write out properly factored statistical expressions representing Bayesian models
Bayesian Models

Bayesian Models

Author: N. Thompson Hobbs, Mevin B. Hooten
Publisher:
ISBN: 0691159289
Pages: 320
Year: 2015-07-27
"This pitch-perfect exposition shows how Bayesian modeling can be used to quantify our uncertain world. Ecologists--and for that matter, scientists everywhere--are aware of these uncertainties, and this book gives them the understanding to do something about it. Hobbs and Hooten take us on a signposted journey through the culture, construction, and consequences of conditional-probability modeling, readying us to take our own scientific journeys through uncertain landscapes."--Noel Cressie, University of Wollongong, Australia "Hobbs and Hooten provide a complete guide to Bayesian thinking and statistics. This is a book by ecologists for ecologists. One of the powers of Bayesian thinking is how it enables you to evaluate knowledge accumulated through multiple experiments and publications, and this excellent primer provides a firm grounding in the hierarchical models that are now the standard approach to evaluating disparate data sets."--Ray Hilborn, University of Washington "In this uniquely well-written and accessible text, Hobbs and Hooten show how to think clearly in a Bayesian framework about data, models, and linking data with models. They provide the necessary tools to develop, implement, and analyze a wide range of ecologically interesting models. There's something new and exciting in this book for every practicing ecologist."--Aaron M. Ellison, Harvard University "Hobbs and Hooten provide an important bridge between standard statistical texts and more advanced Bayesian books, even those aimed at ecologists. Ecological models are complex. Building from likelihood to simple and hierarchical Bayesian models, the authors do a superb job of focusing on concepts, from philosophy to the necessary mathematical and statistical tools. This practical and understandable book belongs on the shelves of all scientists and statisticians interested in ecology."--Jay M. Ver Hoef, Statistician, NOAA-NMFS Alaska Fisheries Science Center "Tackling an important and challenging topic, Hobbs and Hooten provide non-statistically-trained ecologists with the skills they need to use hierarchical Bayesian models accurately and comfortably. The combination of technical explanations and practical examples is great. This book is a valuable contribution that will be widely used."--Benjamin Bolker, McMaster University "This excellent book is one of the best-written and most complete primers on Bayesian hierarchical modeling I have seen. Hobbs and Hooten anticipate many of the common pitfalls and concerns that arise when non-statisticians are introduced to this material. Researchers across a wide range of disciplines will find this book valuable."--Christopher Wikle, University of Missouri
Bayesian Methods for Ecology

Bayesian Methods for Ecology

Author: Michael A. McCarthy
Publisher: Cambridge University Press
ISBN: 113946387X
Pages:
Year: 2007-05-10
The interest in using Bayesian methods in ecology is increasing, however many ecologists have difficulty with conducting the required analyses. McCarthy bridges that gap, using a clear and accessible style. The text also incorporates case studies to demonstrate mark-recapture analysis, development of population models and the use of subjective judgement. The advantages of Bayesian methods, are also described here, for example, the incorporation of any relevant prior information and the ability to assess the evidence in favour of competing hypotheses. Free software is available as well as an accompanying web-site containing the data files and WinBUGS codes. Bayesian Methods for Ecology will appeal to academic researchers, upper undergraduate and graduate students of Ecology.
Introduction to Hierarchical Bayesian Modeling for Ecological Data

Introduction to Hierarchical Bayesian Modeling for Ecological Data

Author: Eric Parent, Etienne Rivot
Publisher: CRC Press
ISBN: 1584889195
Pages: 427
Year: 2012-08-21
Making statistical modeling and inference more accessible to ecologists and related scientists, Introduction to Hierarchical Bayesian Modeling for Ecological Data gives readers a flexible and effective framework to learn about complex ecological processes from various sources of data. It also helps readers get started on building their own statistical models. The text begins with simple models that progressively become more complex and realistic through explanatory covariates and intermediate hidden states variables. When fitting the models to data, the authors gradually present the concepts and techniques of the Bayesian paradigm from a practical point of view using real case studies. They emphasize how hierarchical Bayesian modeling supports multidimensional models involving complex interactions between parameters and latent variables. Data sets, exercises, and R and WinBUGS codes are available on the authors’ website. This book shows how Bayesian statistical modeling provides an intuitive way to organize data, test ideas, investigate competing hypotheses, and assess degrees of confidence of predictions. It also illustrates how conditional reasoning can dismantle a complex reality into more understandable pieces. As conditional reasoning is intimately linked with Bayesian thinking, considering hierarchical models within the Bayesian setting offers a unified and coherent framework for modeling, estimation, and prediction.
Ecological Models and Data in R

Ecological Models and Data in R

Author: Benjamin M. Bolker
Publisher: Princeton University Press
ISBN: 0691125228
Pages: 396
Year: 2008-07-21
Introduction and background; Exploratory data analysis and graphics; Deterministic functions for ecological modeling; Probability and stochastic distributions for ecological modeling; Stochatsic simulation and power analysis; Likelihood and all that; Optimization and all that; Likelihood examples; Standar statistics revisited; Modeling variance; Dynamic models.
Bayesian Population Analysis Using WinBUGS

Bayesian Population Analysis Using WinBUGS

Author: Marc Kéry, Michael Schaub
Publisher: Academic Press
ISBN: 0123870208
Pages: 535
Year: 2012
Bayesian statistics has exploded into biology and its sub-disciplines, such as ecology, over the past decade. The free software program WinBUGS, and its open-source sister OpenBugs, is currently the only flexible and general-purpose program available with which the average ecologist can conduct standard and non-standard Bayesian statistics. Comprehensive and richly commented examples illustrate a wide range of models that are most relevant to the research of a modern population ecologist All WinBUGS/OpenBUGS analyses are completely integrated in software R Includes complete documentation of all R and WinBUGS code required to conduct analyses and shows all the necessary steps from having the data in a text file out of Excel to interpreting and processing the output from WinBUGS in R
Hierarchical Modeling and Inference in Ecology

Hierarchical Modeling and Inference in Ecology

Author: J. Andrew Royle, Robert M. Dorazio
Publisher: Elsevier
ISBN: 0080559255
Pages: 464
Year: 2008-10-15
A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics * Wide variety of examples involving many taxa (birds, amphibians, mammals, insects, plants) * Development of classical, likelihood-based procedures for inference, as well as Bayesian methods of analysis * Detailed explanations describing the implementation of hierarchical models using freely available software such as R and WinBUGS * Computing support in technical appendices in an online companion web site
Introduction to WinBUGS for Ecologists

Introduction to WinBUGS for Ecologists

Author: Marc Kery
Publisher: Academic Press
ISBN: 0123786061
Pages: 320
Year: 2010-07-19
Introduction to WinBUGS for Ecologists introduces applied Bayesian modeling to ecologists using the highly acclaimed, free WinBUGS software. It offers an understanding of statistical models as abstract representations of the various processes that give rise to a data set. Such an understanding is basic to the development of inference models tailored to specific sampling and ecological scenarios. The book begins by presenting the advantages of a Bayesian approach to statistics and introducing the WinBUGS software. It reviews the four most common statistical distributions: the normal, the uniform, the binomial, and the Poisson. It describes the two different kinds of analysis of variance (ANOVA): one-way and two- or multiway. It looks at the general linear model, or ANCOVA, in R and WinBUGS. It introduces generalized linear model (GLM), i.e., the extension of the normal linear model to allow error distributions other than the normal. The GLM is then extended contain additional sources of random variation to become a generalized linear mixed model (GLMM) for a Poisson example and for a binomial example. The final two chapters showcase two fairly novel and nonstandard versions of a GLMM. The first is the site-occupancy model for species distributions; the second is the binomial (or N-) mixture model for estimation and modeling of abundance. Introduction to the essential theories of key models used by ecologists Complete juxtaposition of classical analyses in R and Bayesian analysis of the same models in WinBUGS Provides every detail of R and WinBUGS code required to conduct all analyses Companion Web Appendix that contains all code contained in the book and additional material (including more code and solutions to exercises)
Elements of Mathematical Ecology

Elements of Mathematical Ecology

Author: Mark Kot
Publisher: Cambridge University Press
ISBN: 1316584054
Pages:
Year: 2001-07-19
Elements of Mathematical Ecology provides an introduction to classical and modern mathematical models, methods, and issues in population ecology. The first part of the book is devoted to simple, unstructured population models that ignore much of the variability found in natural populations for the sake of tractability. Topics covered include density dependence, bifurcations, demographic stochasticity, time delays, population interactions (predation, competition, and mutualism), and the application of optimal control theory to the management of renewable resources. The second part of this book is devoted to structured population models, covering spatially-structured population models (with a focus on reaction-diffusion models), age-structured models, and two-sex models. Suitable for upper level students and beginning researchers in ecology, mathematical biology and applied mathematics, the volume includes numerous clear line diagrams that clarify the mathematics, relevant problems thoughout the text that aid understanding, and supplementary mathematical and historical material that enrich the main text.
Handbook of Meta-analysis in Ecology and Evolution

Handbook of Meta-analysis in Ecology and Evolution

Author: Julia Koricheva, Jessica Gurevitch, Kerrie Mengersen
Publisher: Princeton University Press
ISBN: 1400846188
Pages: 520
Year: 2013-04-21
Meta-analysis is a powerful statistical methodology for synthesizing research evidence across independent studies. This is the first comprehensive handbook of meta-analysis written specifically for ecologists and evolutionary biologists, and it provides an invaluable introduction for beginners as well as an up-to-date guide for experienced meta-analysts. The chapters, written by renowned experts, walk readers through every step of meta-analysis, from problem formulation to the presentation of the results. The handbook identifies both the advantages of using meta-analysis for research synthesis and the potential pitfalls and limitations of meta-analysis (including when it should not be used). Different approaches to carrying out a meta-analysis are described, and include moment and least-square, maximum likelihood, and Bayesian approaches, all illustrated using worked examples based on real biological datasets. This one-of-a-kind resource is uniquely tailored to the biological sciences, and will provide an invaluable text for practitioners from graduate students and senior scientists to policymakers in conservation and environmental management. Walks you through every step of carrying out a meta-analysis in ecology and evolutionary biology, from problem formulation to result presentation Brings together experts from a broad range of fields Shows how to avoid, minimize, or resolve pitfalls such as missing data, publication bias, varying data quality, nonindependence of observations, and phylogenetic dependencies among species Helps you choose the right software Draws on numerous examples based on real biological datasets
Animal Movement

Animal Movement

Author: Mevin B. Hooten, Devin S. Johnson, Brett T. McClintock, Juan M. Morales
Publisher: CRC Press
ISBN: 1466582154
Pages: 320
Year: 2017-03-16
The study of animal movement has always been a key element in ecological science, because it is inherently linked to critical processes that scale from individuals to populations and communities to ecosystems. Rapid improvements in biotelemetry data collection and processing technology have given rise to a variety of statistical methods for characterizing animal movement. The book serves as a comprehensive reference for the types of statistical models used to study individual-based animal movement. Animal Movement is an essential reference for wildlife biologists, quantitative ecologists, and statisticians who seek a deeper understanding of modern animal movement models. A wide variety of modeling approaches are reconciled in the book using a consistent notation. Models are organized into groups based on how they treat the underlying spatio-temporal process of movement. Connections among approaches are highlighted to allow the reader to form a broader view of animal movement analysis and its associations with traditional spatial and temporal statistical modeling. After an initial overview examining the role that animal movement plays in ecology, a primer on spatial and temporal statistics provides a solid foundation for the remainder of the book. Each subsequent chapter outlines a fundamental type of statistical model utilized in the contemporary analysis of telemetry data for animal movement inference. Descriptions begin with basic traditional forms and sequentially build up to general classes of models in each category. Important background and technical details for each class of model are provided, including spatial point process models, discrete-time dynamic models, and continuous-time stochastic process models. The book also covers the essential elements for how to accommodate multiple sources of uncertainty, such as location error and latent behavior states. In addition to thorough descriptions of animal movement models, differences and connections are also emphasized to provide a broader perspective of approaches.
A Primer of Ecological Statistics

A Primer of Ecological Statistics

Author: Nicholas J. Gotelli, Aaron M. Ellison
Publisher: Sinauer Associates Incorporated
ISBN: 1605350648
Pages: 614
Year: 2013
This book takes a broad-based approach that emphasizes the historical, cultural, political, religious, social, and economic factors that underlie an understanding of both global and domestic terrorism. This unique text-reader combines original essays with the best of the existing literature on terrorism. Each chapter of this text begins with an overview essay written by the authors, followed by two relevant and engaging articles culled from a wide variety of popular, academic, and governmental sources. This is the only major terrorism text to incorporate readings from top terrorism experts into a traditional textbook format, allowing readers to deepen their understanding of each aspect of terrorism.
A Critique for Ecology

A Critique for Ecology

Author: Robert Henry Peters
Publisher: Cambridge University Press
ISBN: 0521395887
Pages: 366
Year: 1991-07-26
This is a book of criticism. It is directed at contemporary ecology, but would apply to any science or indeed any statement that claims to contain information. Application of simple criteria to judge the information in ecological statements reveals deep inadequacies in the science. Furthermore, the complexity of the contemporary field of ecology and the mistraining of a generation of ecologists has obscured its weakness. As a result, many ecologists are unaware of the failings of the science although others are deeply concerned for the future of the field. The author, Professor Peters, argues that a return to simple question of fact, to observations, and to questions of general relevance to science and society can make ecology a useful, practical and informative science. Such science is desperately needed to meet the problems of the age. A thought-provoking book that will be of interest to all scientists, but in particular ecologists from undergraduates to senior academics and professionals.
Handbook of Spatial Point-Pattern Analysis in Ecology

Handbook of Spatial Point-Pattern Analysis in Ecology

Author: Thorsten Wiegand, Kirk A. Moloney
Publisher: CRC Press
ISBN: 1420082558
Pages: 538
Year: 2013-12-20
Understand How to Analyze and Interpret Information in Ecological Point Patterns Although numerous statistical methods for analyzing spatial point patterns have been available for several decades, they haven’t been extensively applied in an ecological context. Addressing this gap, Handbook of Spatial Point-Pattern Analysis in Ecology shows how the techniques of point-pattern analysis are useful for tackling ecological problems. Within an ecological framework, the book guides readers through a variety of methods for different data types and aids in the interpretation of the results obtained by point-pattern analysis. Ideal for empirical ecologists who want to avoid advanced theoretical literature, the book covers statistical techniques for analyzing and interpreting the information contained in ecological patterns. It presents methods used to extract information hidden in spatial point-pattern data that may point to the underlying processes. The authors focus on point processes and null models that have proven their immediate utility for broad ecological applications, such as cluster processes. Along with the techniques, the handbook provides a comprehensive selection of real-world examples. Most of the examples are analyzed using Programita, a continuously updated software package based on the authors’ many years of teaching and collaborative research in ecological point-pattern analysis. Programita is tailored to meet the needs of real-world applications in ecology. The software and a manual are available online.
Individual-based Modeling and Ecology

Individual-based Modeling and Ecology

Author: Volker Grimm, Steven F. Railsback
Publisher: Princeton University Press
ISBN: 1400850622
Pages: 448
Year: 2013-11-28
Individual-based models are an exciting and widely used new tool for ecology. These computational models allow scientists to explore the mechanisms through which population and ecosystem ecology arises from how individuals interact with each other and their environment. This book provides the first in-depth treatment of individual-based modeling and its use to develop theoretical understanding of how ecological systems work, an approach the authors call "individual-based ecology." Grimm and Railsback start with a general primer on modeling: how to design models that are as simple as possible while still allowing specific problems to be solved, and how to move efficiently through a cycle of pattern-oriented model design, implementation, and analysis. Next, they address the problems of theory and conceptual framework for individual-based ecology: What is "theory"? That is, how do we develop reusable models of how system dynamics arise from characteristics of individuals? What conceptual framework do we use when the classical differential equation framework no longer applies? An extensive review illustrates the ecological problems that have been addressed with individual-based models. The authors then identify how the mechanics of building and using individual-based models differ from those of traditional science, and provide guidance on formulating, programming, and analyzing models. This book will be helpful to ecologists interested in modeling, and to other scientists interested in agent-based modeling.