Bringing Bayesian Models to Life

Bringing Bayesian Models to Life
Author: Mevin B. Hooten
Publisher: CRC Press
Total Pages: 591
Release: 2019-05-15
Genre: Science
ISBN: 0429513372

Download Bringing Bayesian Models to Life Book in PDF, Epub and Kindle

Bringing Bayesian Models to Life empowers the reader to extend, enhance, and implement statistical models for ecological and environmental data analysis. We open the black box and show the reader how to connect modern statistical models to computer algorithms. These algorithms allow the user to fit models that answer their scientific questions without needing to rely on automated Bayesian software. We show how to handcraft statistical models that are useful in ecological and environmental science including: linear and generalized linear models, spatial and time series models, occupancy and capture-recapture models, animal movement models, spatio-temporal models, and integrated population-models. Features: R code implementing algorithms to fit Bayesian models using real and simulated data examples. A comprehensive review of statistical models commonly used in ecological and environmental science. Overview of Bayesian computational methods such as importance sampling, MCMC, and HMC. Derivations of the necessary components to construct statistical algorithms from scratch. Bringing Bayesian Models to Life contains a comprehensive treatment of models and associated algorithms for fitting the models to data. We provide detailed and annotated R code in each chapter and apply it to fit each model we present to either real or simulated data for instructional purposes. Our code shows how to create every result and figure in the book so that readers can use and modify it for their own analyses. We provide all code and data in an organized set of directories available at the authors' websites.

Bayesian Models

Bayesian Models
Author: N. Thompson Hobbs
Publisher: Princeton University Press
Total Pages: 315
Release: 2015-08-04
Genre: Science
ISBN: 1400866553

Download Bayesian Models Book in PDF, Epub and Kindle

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

Bayes Rules!

Bayes Rules!
Author: Alicia A. Johnson
Publisher: CRC Press
Total Pages: 543
Release: 2022-03-03
Genre: Mathematics
ISBN: 1000529509

Download Bayes Rules! Book in PDF, Epub and Kindle

Praise for Bayes Rules!: An Introduction to Applied Bayesian Modeling “A thoughtful and entertaining book, and a great way to get started with Bayesian analysis.” Andrew Gelman, Columbia University “The examples are modern, and even many frequentist intro books ignore important topics (like the great p-value debate) that the authors address. The focus on simulation for understanding is excellent.” Amy Herring, Duke University “I sincerely believe that a generation of students will cite this book as inspiration for their use of – and love for – Bayesian statistics. The narrative holds the reader’s attention and flows naturally – almost conversationally. Put simply, this is perhaps the most engaging introductory statistics textbook I have ever read. [It] is a natural choice for an introductory undergraduate course in applied Bayesian statistics." Yue Jiang, Duke University “This is by far the best book I’ve seen on how to (and how to teach students to) do Bayesian modeling and understand the underlying mathematics and computation. The authors build intuition and scaffold ideas expertly, using interesting real case studies, insightful graphics, and clear explanations. The scope of this book is vast – from basic building blocks to hierarchical modeling, but the authors’ thoughtful organization allows the reader to navigate this journey smoothly. And impressively, by the end of the book, one can run sophisticated Bayesian models and actually understand the whys, whats, and hows.” Paul Roback, St. Olaf College “The authors provide a compelling, integrated, accessible, and non-religious introduction to statistical modeling using a Bayesian approach. They outline a principled approach that features computational implementations and model assessment with ethical implications interwoven throughout. Students and instructors will find the conceptual and computational exercises to be fresh and engaging.” Nicholas Horton, Amherst College An engaging, sophisticated, and fun introduction to the field of Bayesian statistics, Bayes Rules!: An Introduction to Applied Bayesian Modeling brings the power of modern Bayesian thinking, modeling, and computing to a broad audience. In particular, the book is an ideal resource for advanced undergraduate statistics students and practitioners with comparable experience. Bayes Rules! empowers readers to weave Bayesian approaches into their everyday practice. Discussions and applications are data driven. A natural progression from fundamental to multivariable, hierarchical models emphasizes a practical and generalizable model building process. The evaluation of these Bayesian models reflects the fact that a data analysis does not exist in a vacuum. Features • Utilizes data-driven examples and exercises. • Emphasizes the iterative model building and evaluation process. • Surveys an interconnected range of multivariable regression and classification models. • Presents fundamental Markov chain Monte Carlo simulation. • Integrates R code, including RStan modeling tools and the bayesrules package. • Encourages readers to tap into their intuition and learn by doing. • Provides a friendly and inclusive introduction to technical Bayesian concepts. • Supports Bayesian applications with foundational Bayesian theory.

Probability and Bayesian Modeling

Probability and Bayesian Modeling
Author: Jim Albert
Publisher: CRC Press
Total Pages: 553
Release: 2019-12-06
Genre: Mathematics
ISBN: 1351030132

Download Probability and Bayesian Modeling Book in PDF, Epub and Kindle

Probability and Bayesian Modeling is an introduction to probability and Bayesian thinking for undergraduate students with a calculus background. The first part of the book provides a broad view of probability including foundations, conditional probability, discrete and continuous distributions, and joint distributions. Statistical inference is presented completely from a Bayesian perspective. The text introduces inference and prediction for a single proportion and a single mean from Normal sampling. After fundamentals of Markov Chain Monte Carlo algorithms are introduced, Bayesian inference is described for hierarchical and regression models including logistic regression. The book presents several case studies motivated by some historical Bayesian studies and the authors’ research. This text reflects modern Bayesian statistical practice. Simulation is introduced in all the probability chapters and extensively used in the Bayesian material to simulate from the posterior and predictive distributions. One chapter describes the basic tenets of Metropolis and Gibbs sampling algorithms; however several chapters introduce the fundamentals of Bayesian inference for conjugate priors to deepen understanding. Strategies for constructing prior distributions are described in situations when one has substantial prior information and for cases where one has weak prior knowledge. One chapter introduces hierarchical Bayesian modeling as a practical way of combining data from different groups. There is an extensive discussion of Bayesian regression models including the construction of informative priors, inference about functions of the parameters of interest, prediction, and model selection. The text uses JAGS (Just Another Gibbs Sampler) as a general-purpose computational method for simulating from posterior distributions for a variety of Bayesian models. An R package ProbBayes is available containing all of the book datasets and special functions for illustrating concepts from the book. A complete solutions manual is available for instructors who adopt the book in the Additional Resources section.

Statistical Modeling With R

Statistical Modeling With R
Author: Pablo Inchausti
Publisher: Oxford University Press
Total Pages: 519
Release: 2022-11-02
Genre: Science
ISBN: 0192675036

Download Statistical Modeling With R Book in PDF, Epub and Kindle

To date, statistics has tended to be neatly divided into two theoretical approaches or frameworks: frequentist (or classical) and Bayesian. Scientists typically choose the statistical framework to analyse their data depending on the nature and complexity of the problem, and based on their personal views and prior training on probability and uncertainty. Although textbooks and courses should reflect and anticipate this dual reality, they rarely do so. This accessible textbook explains, discusses, and applies both the frequentist and Bayesian theoretical frameworks to fit the different types of statistical models that allow an analysis of the types of data most commonly gathered by life scientists. It presents the material in an informal, approachable, and progressive manner suitable for readers with only a basic knowledge of calculus and statistics. Statistical Modeling with R is aimed at senior undergraduate and graduate students, professional researchers, and practitioners throughout the life sciences, seeking to strengthen their understanding of quantitative methods and to apply them successfully to real world scenarios, whether in the fields of ecology, evolution, environmental studies, or computational biology.

Applied Statistical Modelling for Ecologists

Applied Statistical Modelling for Ecologists
Author: Marc Kéry
Publisher: Elsevier
Total Pages: 551
Release: 2024-07-18
Genre: Science
ISBN: 0443137161

Download Applied Statistical Modelling for Ecologists Book in PDF, Epub and Kindle

Applied Statistical Modelling for Ecologists: A Practical Guide to Bayesian and Likelihood Inference Using R, JAGS/Nimble, Stan and TMB provides an important guide and comparison of powerful new software packages that are now widely used in research publications, including JAGS, Stan, Nimble, and TMB. It provides a gentle introduction to the most exciting specialist software that is often used to conduct cutting-edge research, along with Bayesian statistics and frequentist statistics with its maximum likelihood estimation method. In addition, this book is simple and accessible, allowing researchers to carry out and understand statistical modeling. Through examples, the book covers the underlying statistical models widely used by scientists across many disciplines. Thus, this book will be useful for anyone who needs to quickly become proficient in statistical modeling, and in the model-fitting engines covered. Provides a comprehensive, applied introduction to some of the most exciting, cutting-edge model fitting software packages: JAGS, Nimble, Stan, and TMB Covers all the basics of the modern applied statistical modeling that have become a key part of any natural science, including linear, generalized linear, mixed and also hierarchical models Provides applied introduction to the two dominant methods of parametric statistical modeling: maximum likelihood and Bayesian inference Adopts what could be called a "Rosetta stone approach," wherein understanding of one software, and of its associated language, will be greatly enhanced by seeing the analogous code in one of the other engines

Bayesian Models

Bayesian Models
Author: Mevin B. Hooten
Publisher:
Total Pages: 0
Release: 2025-06-03
Genre: Mathematics
ISBN: 9780691250120

Download Bayesian Models Book in PDF, Epub and Kindle

A fully updated and expanded edition of the essential primer on Bayesian modeling for ecologists Uniquely suited to deal with complexity in a statistically coherent way, Bayesian modeling has become an indispensable tool for ecological research. This book teaches the basic principles of mathematics and statistics needed to apply Bayesian models to the analysis of ecological data, using language non-statisticians can understand. Deemphasizing computer coding in favor of a clear treatment of model building, it starts with a definition of probability and proceeds step-by-step through distribution theory, likelihood, simple Bayesian models, and hierarchical Bayesian models. Now revised and expanded, Bayesian Models enables students and practitioners to gain new insights from ecological models and data properly tempered by uncertainty. Covers the basic rules of probability needed to model diverse types of ecological data in the Bayesian framework Shows how to write proper mathematical expressions for posterior distributions using directed acyclic graphs as templates Explains how to use the powerful Markov chain Monte Carlo algorithm to find posterior distributions of model parameters, latent states, and missing data Teaches how to check models to assure they meet the assumptions of model-based inference Demonstrates how to make inferences from single and multiple Bayesian models Provides worked problems for practicing and strengthening modeling skills Features new chapters on spatial models and modeling missing data

Bayesian Models for Categorical Data

Bayesian Models for Categorical Data
Author: Peter Congdon
Publisher: John Wiley & Sons
Total Pages: 446
Release: 2005-12-13
Genre: Mathematics
ISBN: 0470092386

Download Bayesian Models for Categorical Data Book in PDF, Epub and Kindle

The use of Bayesian methods for the analysis of data has grown substantially in areas as diverse as applied statistics, psychology, economics and medical science. Bayesian Methods for Categorical Data sets out to demystify modern Bayesian methods, making them accessible to students and researchers alike. Emphasizing the use of statistical computing and applied data analysis, this book provides a comprehensive introduction to Bayesian methods of categorical outcomes. * Reviews recent Bayesian methodology for categorical outcomes (binary, count and multinomial data). * Considers missing data models techniques and non-standard models (ZIP and negative binomial). * Evaluates time series and spatio-temporal models for discrete data. * Features discussion of univariate and multivariate techniques. * Provides a set of downloadable worked examples with documented WinBUGS code, available from an ftp site. The author's previous 2 bestselling titles provided a comprehensive introduction to the theory and application of Bayesian models. Bayesian Models for Categorical Data continues to build upon this foundation by developing their application to categorical, or discrete data - one of the most common types of data available. The author's clear and logical approach makes the book accessible to a wide range of students and practitioners, including those dealing with categorical data in medicine, sociology, psychology and epidemiology.

Bayes Rules!

Bayes Rules!
Author: Alicia A. Johnson
Publisher: CRC Press
Total Pages: 606
Release: 2022-03-03
Genre: Mathematics
ISBN: 1000529568

Download Bayes Rules! Book in PDF, Epub and Kindle

Praise for Bayes Rules!: An Introduction to Applied Bayesian Modeling “A thoughtful and entertaining book, and a great way to get started with Bayesian analysis.” Andrew Gelman, Columbia University “The examples are modern, and even many frequentist intro books ignore important topics (like the great p-value debate) that the authors address. The focus on simulation for understanding is excellent.” Amy Herring, Duke University “I sincerely believe that a generation of students will cite this book as inspiration for their use of – and love for – Bayesian statistics. The narrative holds the reader’s attention and flows naturally – almost conversationally. Put simply, this is perhaps the most engaging introductory statistics textbook I have ever read. [It] is a natural choice for an introductory undergraduate course in applied Bayesian statistics." Yue Jiang, Duke University “This is by far the best book I’ve seen on how to (and how to teach students to) do Bayesian modeling and understand the underlying mathematics and computation. The authors build intuition and scaffold ideas expertly, using interesting real case studies, insightful graphics, and clear explanations. The scope of this book is vast – from basic building blocks to hierarchical modeling, but the authors’ thoughtful organization allows the reader to navigate this journey smoothly. And impressively, by the end of the book, one can run sophisticated Bayesian models and actually understand the whys, whats, and hows.” Paul Roback, St. Olaf College “The authors provide a compelling, integrated, accessible, and non-religious introduction to statistical modeling using a Bayesian approach. They outline a principled approach that features computational implementations and model assessment with ethical implications interwoven throughout. Students and instructors will find the conceptual and computational exercises to be fresh and engaging.” Nicholas Horton, Amherst College An engaging, sophisticated, and fun introduction to the field of Bayesian statistics, Bayes Rules!: An Introduction to Applied Bayesian Modeling brings the power of modern Bayesian thinking, modeling, and computing to a broad audience. In particular, the book is an ideal resource for advanced undergraduate statistics students and practitioners with comparable experience. Bayes Rules! empowers readers to weave Bayesian approaches into their everyday practice. Discussions and applications are data driven. A natural progression from fundamental to multivariable, hierarchical models emphasizes a practical and generalizable model building process. The evaluation of these Bayesian models reflects the fact that a data analysis does not exist in a vacuum. Features • Utilizes data-driven examples and exercises. • Emphasizes the iterative model building and evaluation process. • Surveys an interconnected range of multivariable regression and classification models. • Presents fundamental Markov chain Monte Carlo simulation. • Integrates R code, including RStan modeling tools and the bayesrules package. • Encourages readers to tap into their intuition and learn by doing. • Provides a friendly and inclusive introduction to technical Bayesian concepts. • Supports Bayesian applications with foundational Bayesian theory.

Introduction to Hierarchical Bayesian Modeling for Ecological Data

Introduction to Hierarchical Bayesian Modeling for Ecological Data
Author: Eric Parent
Publisher: CRC Press
Total Pages: 429
Release: 2012-08-21
Genre: Mathematics
ISBN: 1584889195

Download Introduction to Hierarchical Bayesian Modeling for Ecological Data Book in PDF, Epub and Kindle

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.