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Applied Hierarchical Modeling In Ecology

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Hierarchical Modeling and Inference in Ecology

Hierarchical Modeling and Inference in Ecology Book
Author : J. Andrew Royle,Robert M. Dorazio
Publisher : Elsevier
Release : 2008-10-15
ISBN : 0080559255
Language : En, Es, Fr & De

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Book Description :

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

Applied Hierarchical Modeling in Ecology Analysis of Distribution Abundance and Species Richness in R and BUGS

Applied Hierarchical Modeling in Ecology  Analysis of Distribution  Abundance and Species Richness in R and BUGS Book
Author : Marc Kery,J. Andrew Royle
Publisher : Academic Press
Release : 2020-10-10
ISBN : 0128097272
Language : En, Es, Fr & De

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Book Description :

Applied Hierarchical Modeling in Ecology: Analysis of Distribution, Abundance and Species Richness in R and BUGS, Volume Two: Dynamic and Advanced Models provides a synthesis of the state-of-the-art in hierarchical models for plant and animal distribution, also focusing on the complex and more advanced models currently available. The book explains all procedures in the context of hierarchical models that represent a unified approach to ecological research, thus taking the reader from design, through data collection, and into analyses using a very powerful way of synthesizing data. Makes ecological modeling accessible to people who are struggling to use complex or advanced modeling programs Synthesizes current ecological models and explains how they are inter-connected Contains numerous examples throughout the book, walking the reading through scenarios with both real and simulated data Provides an ideal resource for ecologists working in R software and in BUGS software for more flexible Bayesian analyses

Applied Hierarchical Modeling in Ecology Analysis of distribution abundance and species richness in R and BUGS

Applied Hierarchical Modeling in Ecology  Analysis of distribution  abundance and species richness in R and BUGS Book
Author : Marc Kery,J. Andrew Royle
Publisher : Academic Press
Release : 2015-11-14
ISBN : 0128014865
Language : En, Es, Fr & De

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Book Description :

Applied Hierarchical Modeling in Ecology: Distribution, Abundance, Species Richness offers a new synthesis of the state-of-the-art of hierarchical models for plant and animal distribution, abundance, and community characteristics such as species richness using data collected in metapopulation designs. These types of data are extremely widespread in ecology and its applications in such areas as biodiversity monitoring and fisheries and wildlife management. This first volume explains static models/procedures in the context of hierarchical models that collectively represent a unified approach to ecological research, taking the reader from design, through data collection, and into analyses using a very powerful class of models. Applied Hierarchical Modeling in Ecology, Volume 1 serves as an indispensable manual for practicing field biologists, and as a graduate-level text for students in ecology, conservation biology, fisheries/wildlife management, and related fields. Provides a synthesis of important classes of models about distribution, abundance, and species richness while accommodating imperfect detection Presents models and methods for identifying unmarked individuals and species Written in a step-by-step approach accessible to non-statisticians and provides fully worked examples that serve as a template for readers' analyses Includes companion website containing data sets, code, solutions to exercises, and further information

Introduction to Hierarchical Bayesian Modeling for Ecological Data

Introduction to Hierarchical Bayesian Modeling for Ecological Data Book
Author : Eric Parent,Etienne Rivot
Publisher : CRC Press
Release : 2012-08-21
ISBN : 1584889195
Language : En, Es, Fr & De

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Book Description :

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.

Bayesian Population Analysis using WinBUGS

Bayesian Population Analysis using WinBUGS Book
Author : Marc Kery,Michael Schaub
Publisher : Academic Press
Release : 2011-10-11
ISBN : 0123870216
Language : En, Es, Fr & De

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Book Description :

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

Introduction to WinBUGS for Ecologists

Introduction to WinBUGS for Ecologists Book
Author : Marc Kery
Publisher : Academic Press
Release : 2010-07-19
ISBN : 9780123786067
Language : En, Es, Fr & De

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Book Description :

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)

Ecological Models and Data in R

Ecological Models and Data in R Book
Author : Benjamin M. Bolker
Publisher : Princeton University Press
Release : 2008-07-21
ISBN : 0691125228
Language : En, Es, Fr & De

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Book Description :

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.

Integrated Population Models

Integrated Population Models Book
Author : Michael Schaub,Marc Kery
Publisher : Academic Press
Release : 2021-11-23
ISBN : 0128209151
Language : En, Es, Fr & De

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Book Description :

Integrated Population Models: Theory and Ecological Applications with R and JAGS is the first book on integrated population models, which constitute a powerful framework for combining multiple data sets from the population and the individual levels to estimate demographic parameters, and population size and trends. These models identify drivers of population dynamics and forecast the composition and trajectory of a population. Written by two population ecologists with expertise on integrated population modeling, this book provides a comprehensive synthesis of the relevant theory of integrated population models with an extensive overview of practical applications, using Bayesian methods by means of case studies. The book contains fully-documented, complete code for fitting all models in the free software, R and JAGS. It also includes all required code for pre- and post-model-fitting analysis. Integrated Population Models is an invaluable reference for researchers and practitioners involved in population analysis, and for graduate-level students in ecology, conservation biology, wildlife management, and related fields. The text is ideal for self-study and advanced graduate-level courses. Offers practical and accessible ecological applications of IPMs (integrated population models) Provides full documentation of analyzed code in the Bayesian framework Written and structured for an easy approach to the subject, especially for non-statisticians

Joint Species Distribution Modelling

Joint Species Distribution Modelling Book
Author : Otso Ovaskainen,Nerea Abrego
Publisher : Cambridge University Press
Release : 2020-06-11
ISBN : 1108492460
Language : En, Es, Fr & De

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Book Description :

A comprehensive account of joint species distribution modelling, covering statistical analyses in light of modern community ecology theory.

Spatial Capture Recapture

Spatial Capture Recapture Book
Author : J. Andrew Royle,Richard B. Chandler,Rahel Sollmann,Beth Gardner
Publisher : Academic Press
Release : 2013-08-27
ISBN : 012407152X
Language : En, Es, Fr & De

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Book Description :

Spatial Capture-Recapture provides a comprehensive how-to manual with detailed examples of spatial capture-recapture models based on current technology and knowledge. Spatial Capture-Recapture provides you with an extensive step-by-step analysis of many data sets using different software implementations. The authors' approach is practical – it embraces Bayesian and classical inference strategies to give the reader different options to get the job done. In addition, Spatial Capture-Recapture provides data sets, sample code and computing scripts in an R package. Comprehensive reference on revolutionary new methods in ecology makes this the first and only book on the topic Every methodological element has a detailed worked example with a code template, allowing you to learn by example Includes an R package that contains all computer code and data sets on companion website

Hierarchical Modeling and Analysis for Spatial Data

Hierarchical Modeling and Analysis for Spatial Data Book
Author : Sudipto Banerjee
Publisher : CRC Press
Release : 2003-12-17
ISBN : 020348780X
Language : En, Es, Fr & De

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Book Description :

Among the many uses of hierarchical modeling, their application to the statistical analysis of spatial and spatio-temporal data from areas such as epidemiology And environmental science has proven particularly fruitful. Yet to date, the few books that address the subject have been either too narrowly focused on specific aspects of spatial analysis,

Occupancy Estimation and Modeling

Occupancy Estimation and Modeling Book
Author : Darryl I. MacKenzie,James D. Nichols,J. Andrew Royle,Kenneth H. Pollock,Larissa Bailey,James E. Hines
Publisher : Elsevier
Release : 2017-11-17
ISBN : 0124072453
Language : En, Es, Fr & De

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Book Description :

Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition, provides a synthesis of model-based approaches for analyzing presence-absence data, allowing for imperfect detection. Beginning from the relatively simple case of estimating the proportion of area or sampling units occupied at the time of surveying, the authors describe a wide variety of extensions that have been developed since the early 2000s. This provides an improved insight about species and community ecology, including, detection heterogeneity; correlated detections; spatial autocorrelation; multiple states or classes of occupancy; changes in occupancy over time; species co-occurrence; community-level modeling, and more. Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence, Second Edition has been greatly expanded and detail is provided regarding the estimation methods and examples of their application are given. Important study design recommendations are also covered to give a well rounded view of modeling. Provides authoritative insights into the latest in occupancy modeling Examines the latest methods in analyzing detection/no detection data surveys Addresses critical issues of imperfect detectability and its effects on species occurrence estimation Discusses important study design considerations such as defining sample units, sample size determination and optimal effort allocation

Bayesian Models

Bayesian Models Book
Author : N. Thompson Hobbs,Mevin Hooten
Publisher : Princeton University Press
Release : 2015-08-04
ISBN : 1400866553
Language : En, Es, Fr & De

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Book Description :

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

Models of the Ecological Hierarchy

Models of the Ecological Hierarchy Book
Author : Ferenc Jordan
Publisher : Newnes
Release : 2012-11-29
ISBN : 0444593969
Language : En, Es, Fr & De

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Book Description :

"Based on selected papers covering the presentations at the 7th European Conference on Ecological Modelling, organized by ISEM and hosted by The Microsoft Research--University of Trento Center for Computational and Systems Biology from 30 May to 2 June, 2011 in Riva del Garde, Italy"--P. xi.

Mixed Effects Models and Extensions in Ecology with R

Mixed Effects Models and Extensions in Ecology with R Book
Author : Alain Zuur,Elena N. Ieno,Neil Walker,Anatoly A. Saveliev,Graham M. Smith
Publisher : Springer Science & Business Media
Release : 2009-03-05
ISBN : 0387874585
Language : En, Es, Fr & De

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Book Description :

This book discusses advanced statistical methods that can be used to analyse ecological data. Most environmental collected data are measured repeatedly over time, or space and this requires the use of GLMM or GAMM methods. The book starts by revising regression, additive modelling, GAM and GLM, and then discusses dealing with spatial or temporal dependencies and nested data.

Bayesian Data Analysis in Ecology Using Linear Models with R BUGS and Stan

Bayesian Data Analysis in Ecology Using Linear Models with R  BUGS  and Stan Book
Author : Franzi Korner-Nievergelt,Tobias Roth,Stefanie von Felten,Jérôme Guélat,Bettina Almasi,Pius Korner-Nievergelt
Publisher : Academic Press
Release : 2015-04-04
ISBN : 0128016787
Language : En, Es, Fr & De

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Book Description :

Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN examines the Bayesian and frequentist methods of conducting data analyses. The book provides the theoretical background in an easy-to-understand approach, encouraging readers to examine the processes that generated their data. Including discussions of model selection, model checking, and multi-model inference, the book also uses effect plots that allow a natural interpretation of data. Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN introduces Bayesian software, using R for the simple modes, and flexible Bayesian software (BUGS and Stan) for the more complicated ones. Guiding the ready from easy toward more complex (real) data analyses ina step-by-step manner, the book presents problems and solutions—including all R codes—that are most often applicable to other data and questions, making it an invaluable resource for analyzing a variety of data types. Introduces Bayesian data analysis, allowing users to obtain uncertainty measurements easily for any derived parameter of interest Written in a step-by-step approach that allows for eased understanding by non-statisticians Includes a companion website containing R-code to help users conduct Bayesian data analyses on their own data All example data as well as additional functions are provided in the R-package blmeco

Spatial and Spatio temporal Bayesian Models with R INLA

Spatial and Spatio temporal Bayesian Models with R   INLA Book
Author : Marta Blangiardo,Michela Cameletti
Publisher : John Wiley & Sons
Release : 2015-06-02
ISBN : 1118326555
Language : En, Es, Fr & De

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Book Description :

Spatial and Spatio-Temporal Bayesian Models with R-INLA provides a much needed, practically oriented & innovative presentation of the combination of Bayesian methodology and spatial statistics. The authors combine an introduction to Bayesian theory and methodology with a focus on the spatial and spatio­-temporal models used within the Bayesian framework and a series of practical examples which allow the reader to link the statistical theory presented to real data problems. The numerous examples from the fields of epidemiology, biostatistics and social science all are coded in the R package R-INLA, which has proven to be a valid alternative to the commonly used Markov Chain Monte Carlo simulations

Bayesian Modeling Using WinBUGS

Bayesian Modeling Using WinBUGS Book
Author : Ioannis Ntzoufras
Publisher : John Wiley & Sons
Release : 2011-09-20
ISBN : 1118210352
Language : En, Es, Fr & De

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Book Description :

A hands-on introduction to the principles of Bayesian modeling using WinBUGS Bayesian Modeling Using WinBUGS provides an easily accessible introduction to the use of WinBUGS programming techniques in a variety of Bayesian modeling settings. The author provides an accessible treatment of the topic, offering readers a smooth introduction to the principles of Bayesian modeling with detailed guidance on the practical implementation of key principles. The book begins with a basic introduction to Bayesian inference and the WinBUGS software and goes on to cover key topics, including: Markov Chain Monte Carlo algorithms in Bayesian inference Generalized linear models Bayesian hierarchical models Predictive distribution and model checking Bayesian model and variable evaluation Computational notes and screen captures illustrate the use of both WinBUGS as well as R software to apply the discussed techniques. Exercises at the end of each chapter allow readers to test their understanding of the presented concepts and all data sets and code are available on the book's related Web site. Requiring only a working knowledge of probability theory and statistics, Bayesian Modeling Using WinBUGS serves as an excellent book for courses on Bayesian statistics at the upper-undergraduate and graduate levels. It is also a valuable reference for researchers and practitioners in the fields of statistics, actuarial science, medicine, and the social sciences who use WinBUGS in their everyday work.

Mathematical Modeling in Economics Ecology and the Environment

Mathematical Modeling in Economics  Ecology and the Environment Book
Author : N.V. Hritonenko,Yuri P. Yatsenko
Publisher : Springer Science & Business Media
Release : 2013-04-17
ISBN : 1441997334
Language : En, Es, Fr & De

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Book Description :

The problems of interrelation between human economics and natural environment include scientific, technical, economic, demographic, social, political and other aspects that are studied by scientists of many specialities. One of the important aspects in scientific study of environmental and ecological problems is the development of mathematical and computer tools for rational management of economics and environment. This book introduces a wide range of mathematical models in economics, ecology and environmental sciences to a general mathematical audience with no in-depth experience in this specific area. Areas covered are: controlled economic growth and technological development, world dynamics, environmental impact, resource extraction, air and water pollution propagation, ecological population dynamics and exploitation. A variety of known models are considered, from classical ones (Cobb Douglass production function, Leontief input-output analysis, Solow models of economic dynamics, Verhulst-Pearl and Lotka-Volterra models of population dynamics, and others) to the models of world dynamics and the models of water contamination propagation used after Chemobyl nuclear catastrophe. Special attention is given to modelling of hierarchical regional economic-ecological interaction and technological change in the context of environmental impact. Xlll XIV Construction of Mathematical Models ...

Models for Ecological Data

Models for Ecological Data Book
Author : James S. Clark
Publisher : Princeton University Press
Release : 2020-10-06
ISBN : 0691220123
Language : En, Es, Fr & De

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Book Description :

The environmental sciences are undergoing a revolution in the use of models and data. Facing ecological data sets of unprecedented size and complexity, environmental scientists are struggling to understand and exploit powerful new statistical tools for making sense of ecological processes. In Models for Ecological Data, James Clark introduces ecologists to these modern methods in modeling and computation. Assuming only basic courses in calculus and statistics, the text introduces readers to basic maximum likelihood and then works up to more advanced topics in Bayesian modeling and computation. Clark covers both classical statistical approaches and powerful new computational tools and describes how complexity can motivate a shift from classical to Bayesian methods. Through an available lab manual, the book introduces readers to the practical work of data modeling and computation in the language R. Based on a successful course at Duke University and National Science Foundation-funded institutes on hierarchical modeling, Models for Ecological Data will enable ecologists and other environmental scientists to develop useful models that make sense of ecological data. Consistent treatment from classical to modern Bayes Underlying distribution theory to algorithm development Many examples and applications Does not assume statistical background Extensive supporting appendixes Lab manual in R is available separately