Statistical Modeling Using Bayesian Latent Gaussian Models
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Statistical Modeling Using Bayesian Latent Gaussian Models by Birgir Hrafnkelsson Pdf
This book focuses on the statistical modeling of geophysical and environmental data using Bayesian latent Gaussian models. The structure of these models is described in a thorough introductory chapter, which explains how to construct prior densities for the model parameters, how to infer the parameters using Bayesian computation, and how to use the models to make predictions. The remaining six chapters focus on the application of Bayesian latent Gaussian models to real examples in glaciology, hydrology, engineering seismology, seismology, meteorology and climatology. These examples include: spatial predictions of surface mass balance; the estimation of Antarctica’s contribution to sea-level rise; the estimation of rating curves for the projection of water level to discharge; ground motion models for strong motion; spatial modeling of earthquake magnitudes; weather forecasting based on numerical model forecasts; and extreme value analysis of precipitation on a high-dimensional grid. The book is aimed at graduate students and experts in statistics, geophysics, environmental sciences, engineering, and related fields.
Bayesian Regression Modeling with INLA by Xiaofeng Wang,Yu Ryan Yue,Julian J. Faraway Pdf
INLA stands for Integrated Nested Laplace Approximations, which is a new method for fitting a broad class of Bayesian regression models. No samples of the posterior marginal distributions need to be drawn using INLA, so it is a computationally convenient alternative to Markov chain Monte Carlo (MCMC), the standard tool for Bayesian inference. Bayesian Regression Modeling with INLA covers a wide range of modern regression models and focuses on the INLA technique for building Bayesian models using real-world data and assessing their validity. A key theme throughout the book is that it makes sense to demonstrate the interplay of theory and practice with reproducible studies. Complete R commands are provided for each example, and a supporting website holds all of the data described in the book. An R package including the data and additional functions in the book is available to download. The book is aimed at readers who have a basic knowledge of statistical theory and Bayesian methodology. It gets readers up to date on the latest in Bayesian inference using INLA and prepares them for sophisticated, real-world work. Xiaofeng Wang is Professor of Medicine and Biostatistics at the Cleveland Clinic Lerner College of Medicine of Case Western Reserve University and a Full Staff in the Department of Quantitative Health Sciences at Cleveland Clinic. Yu Ryan Yue is Associate Professor of Statistics in the Paul H. Chook Department of Information Systems and Statistics at Baruch College, The City University of New York. Julian J. Faraway is Professor of Statistics in the Department of Mathematical Sciences at the University of Bath.
Statistical Modeling and Computation by Dirk P. Kroese,Joshua C.C. Chan Pdf
This textbook on statistical modeling and statistical inference will assist advanced undergraduate and graduate students. Statistical Modeling and Computation provides a unique introduction to modern Statistics from both classical and Bayesian perspectives. It also offers an integrated treatment of Mathematical Statistics and modern statistical computation, emphasizing statistical modeling, computational techniques, and applications. Each of the three parts will cover topics essential to university courses. Part I covers the fundamentals of probability theory. In Part II, the authors introduce a wide variety of classical models that include, among others, linear regression and ANOVA models. In Part III, the authors address the statistical analysis and computation of various advanced models, such as generalized linear, state-space and Gaussian models. Particular attention is paid to fast Monte Carlo techniques for Bayesian inference on these models. Throughout the book the authors include a large number of illustrative examples and solved problems. The book also features a section with solutions, an appendix that serves as a MATLAB primer, and a mathematical supplement.
Statistical Modelling and Regression Structures by Thomas Kneib,Gerhard Tutz Pdf
The contributions collected in this book have been written by well-known statisticians to acknowledge Ludwig Fahrmeir's far-reaching impact on Statistics as a science, while celebrating his 65th birthday. The contributions cover broad areas of contemporary statistical model building, including semiparametric and geoadditive regression, Bayesian inference in complex regression models, time series modelling, statistical regularization, graphical models and stochastic volatility models.
Bayesian Statistical Modeling with Stan, R, and Python by Kentaro Matsuura Pdf
This book provides a highly practical introduction to Bayesian statistical modeling with Stan, which has become the most popular probabilistic programming language. The book is divided into four parts. The first part reviews the theoretical background of modeling and Bayesian inference and presents a modeling workflow that makes modeling more engineering than art. The second part discusses the use of Stan, CmdStanR, and CmdStanPy from the very beginning to basic regression analyses. The third part then introduces a number of probability distributions, nonlinear models, and hierarchical (multilevel) models, which are essential to mastering statistical modeling. It also describes a wide range of frequently used modeling techniques, such as censoring, outliers, missing data, speed-up, and parameter constraints, and discusses how to lead convergence of MCMC. Lastly, the fourth part examines advanced topics for real-world data: longitudinal data analysis, state space models, spatial data analysis, Gaussian processes, Bayesian optimization, dimensionality reduction, model selection, and information criteria, demonstrating that Stan can solve any one of these problems in as little as 30 lines. Using numerous easy-to-understand examples, the book explains key concepts, which continue to be useful when using future versions of Stan and when using other statistical modeling tools. The examples do not require domain knowledge and can be generalized to many fields. The book presents full explanations of code and math formulas, enabling readers to extend models for their own problems. All the code and data are on GitHub.
Bayesian Analysis with Python by Osvaldo Martin Pdf
Unleash the power and flexibility of the Bayesian framework About This Book Simplify the Bayes process for solving complex statistical problems using Python; Tutorial guide that will take the you through the journey of Bayesian analysis with the help of sample problems and practice exercises; Learn how and when to use Bayesian analysis in your applications with this guide. Who This Book Is For Students, researchers and data scientists who wish to learn Bayesian data analysis with Python and implement probabilistic models in their day to day projects. Programming experience with Python is essential. No previous statistical knowledge is assumed. What You Will Learn Understand the essentials Bayesian concepts from a practical point of view Learn how to build probabilistic models using the Python library PyMC3 Acquire the skills to sanity-check your models and modify them if necessary Add structure to your models and get the advantages of hierarchical models Find out how different models can be used to answer different data analysis questions When in doubt, learn to choose between alternative models. Predict continuous target outcomes using regression analysis or assign classes using logistic and softmax regression. Learn how to think probabilistically and unleash the power and flexibility of the Bayesian framework In Detail The purpose of this book is to teach the main concepts of Bayesian data analysis. We will learn how to effectively use PyMC3, a Python library for probabilistic programming, to perform Bayesian parameter estimation, to check models and validate them. This book begins presenting the key concepts of the Bayesian framework and the main advantages of this approach from a practical point of view. Moving on, we will explore the power and flexibility of generalized linear models and how to adapt them to a wide array of problems, including regression and classification. We will also look into mixture models and clustering data, and we will finish with advanced topics like non-parametrics models and Gaussian processes. With the help of Python and PyMC3 you will learn to implement, check and expand Bayesian models to solve data analysis problems. Style and approach Bayes algorithms are widely used in statistics, machine learning, artificial intelligence, and data mining. This will be a practical guide allowing the readers to use Bayesian methods for statistical modelling and analysis using Python.
Spatial and Spatio-temporal Bayesian Models with R - INLA by Marta Blangiardo,Michela Cameletti Pdf
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 inference with INLA by Virgilio Gomez-Rubio Pdf
The integrated nested Laplace approximation (INLA) is a recent computational method that can fit Bayesian models in a fraction of the time required by typical Markov chain Monte Carlo (MCMC) methods. INLA focuses on marginal inference on the model parameters of latent Gaussian Markov random fields models and exploits conditional independence properties in the model for computational speed. Bayesian Inference with INLA provides a description of INLA and its associated R package for model fitting. This book describes the underlying methodology as well as how to fit a wide range of models with R. Topics covered include generalized linear mixed-effects models, multilevel models, spatial and spatio-temporal models, smoothing methods, survival analysis, imputation of missing values, and mixture models. Advanced features of the INLA package and how to extend the number of priors and latent models available in the package are discussed. All examples in the book are fully reproducible and datasets and R code are available from the book website. This book will be helpful to researchers from different areas with some background in Bayesian inference that want to apply the INLA method in their work. The examples cover topics on biostatistics, econometrics, education, environmental science, epidemiology, public health, and the social sciences.
Statistical Rethinking: A Bayesian Course with Examples in R and Stan builds readers’ knowledge of and confidence in statistical modeling. Reflecting the need for even minor programming in today’s model-based statistics, the book pushes readers to perform step-by-step calculations that are usually automated. This unique computational approach ensures that readers understand enough of the details to make reasonable choices and interpretations in their own modeling work. The text presents generalized linear multilevel models from a Bayesian perspective, relying on a simple logical interpretation of Bayesian probability and maximum entropy. It covers from the basics of regression to multilevel models. The author also discusses measurement error, missing data, and Gaussian process models for spatial and network autocorrelation. By using complete R code examples throughout, this book provides a practical foundation for performing statistical inference. Designed for both PhD students and seasoned professionals in the natural and social sciences, it prepares them for more advanced or specialized statistical modeling. Web Resource The book is accompanied by an R package (rethinking) that is available on the author’s website and GitHub. The two core functions (map and map2stan) of this package allow a variety of statistical models to be constructed from standard model formulas.
Graphical Models with R by Søren Højsgaard,David Edwards,Steffen Lauritzen Pdf
Graphical models in their modern form have been around since the late 1970s and appear today in many areas of the sciences. Along with the ongoing developments of graphical models, a number of different graphical modeling software programs have been written over the years. In recent years many of these software developments have taken place within the R community, either in the form of new packages or by providing an R interface to existing software. This book attempts to give the reader a gentle introduction to graphical modeling using R and the main features of some of these packages. In addition, the book provides examples of how more advanced aspects of graphical modeling can be represented and handled within R. Topics covered in the seven chapters include graphical models for contingency tables, Gaussian and mixed graphical models, Bayesian networks and modeling high dimensional data.
Bayesian Modeling and Computation in Python by Osvaldo A. Martin,Ravin Kumar,Junpeng Lao Pdf
Bayesian Modeling and Computation in Python aims to help beginner Bayesian practitioners to become intermediate modelers. It uses a hands on approach with PyMC3, Tensorflow Probability, ArviZ and other libraries focusing on the practice of applied statistics with references to the underlying mathematical theory. The book starts with a refresher of the Bayesian Inference concepts. The second chapter introduces modern methods for Exploratory Analysis of Bayesian Models. With an understanding of these two fundamentals the subsequent chapters talk through various models including linear regressions, splines, time series, Bayesian additive regression trees. The final chapters include Approximate Bayesian Computation, end to end case studies showing how to apply Bayesian modelling in different settings, and a chapter about the internals of probabilistic programming languages. Finally the last chapter serves as a reference for the rest of the book by getting closer into mathematical aspects or by extending the discussion of certain topics. This book is written by contributors of PyMC3, ArviZ, Bambi, and Tensorflow Probability among other libraries.
Bayesian Analysis with Python by Osvaldo Martin Pdf
Bayesian modeling with PyMC3 and exploratory analysis of Bayesian models with ArviZ Key FeaturesA step-by-step guide to conduct Bayesian data analyses using PyMC3 and ArviZA modern, practical and computational approach to Bayesian statistical modelingA tutorial for Bayesian analysis and best practices with the help of sample problems and practice exercises.Book Description The second edition of Bayesian Analysis with Python is an introduction to the main concepts of applied Bayesian inference and its practical implementation in Python using PyMC3, a state-of-the-art probabilistic programming library, and ArviZ, a new library for exploratory analysis of Bayesian models. The main concepts of Bayesian statistics are covered using a practical and computational approach. Synthetic and real data sets are used to introduce several types of models, such as generalized linear models for regression and classification, mixture models, hierarchical models, and Gaussian processes, among others. By the end of the book, you will have a working knowledge of probabilistic modeling and you will be able to design and implement Bayesian models for your own data science problems. After reading the book you will be better prepared to delve into more advanced material or specialized statistical modeling if you need to. What you will learnBuild probabilistic models using the Python library PyMC3 Analyze probabilistic models with the help of ArviZ Acquire the skills required to sanity check models and modify them if necessary Understand the advantages and caveats of hierarchical modelsFind out how different models can be used to answer different data analysis questionsCompare models and choose between alternative onesDiscover how different models are unified from a probabilistic perspective Think probabilistically and benefit from the flexibility of the Bayesian frameworkWho this book is for If you are a student, data scientist, researcher, or a developer looking to get started with Bayesian data analysis and probabilistic programming, this book is for you. The book is introductory so no previous statistical knowledge is required, although some experience in using Python and NumPy is expected.
Focusing on Bayesian approaches and computations using simulation-based methods for inference, Time Series: Modeling, Computation, and Inference integrates mainstream approaches for time series modeling with significant recent developments in methodology and applications of time series analysis. It encompasses a graduate-level account of Bayesian time series modeling and analysis, a broad range of references to state-of-the-art approaches to univariate and multivariate time series analysis, and emerging topics at research frontiers. The book presents overviews of several classes of models and related methodology for inference, statistical computation for model fitting and assessment, and forecasting. The authors also explore the connections between time- and frequency-domain approaches and develop various models and analyses using Bayesian tools, such as Markov chain Monte Carlo (MCMC) and sequential Monte Carlo (SMC) methods. They illustrate the models and methods with examples and case studies from a variety of fields, including signal processing, biomedicine, and finance. Data sets, R and MATLAB® code, and other material are available on the authors’ websites. Along with core models and methods, this text offers sophisticated tools for analyzing challenging time series problems. It also demonstrates the growth of time series analysis into new application areas.
Bayes Rules! by Alicia A. Johnson,Miles Q. Ott,Mine Dogucu Pdf
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.
Statistical Modeling and Analysis for Complex Data Problems by Pierre Duchesne,Bruno Rémillard Pdf
STATISTICAL MODELING AND ANALYSIS FOR COMPLEX DATA PROBLEMS treats some of today’s more complex problems and it reflects some of the important research directions in the field. Twenty-nine authors—largely from Montreal’s GERAD Multi-University Research Center and who work in areas of theoretical statistics, applied statistics, probability theory, and stochastic processes—present survey chapters on various theoretical and applied problems of importance and interest to researchers and students across a number of academic domains. Some of the areas and topics examined in the volume are: an analysis of complex survey data, the 2000 American presidential election in Florida, data mining, estimation of uncertainty for machine learning algorithms, interacting stochastic processes, dependent data & copulas, Bayesian analysis of hazard rates, re-sampling methods in a periodic replacement problem, statistical testing in genetics and for dependent data, statistical analysis of time series analysis, theoretical and applied stochastic processes, and an efficient non linear filtering algorithm for the position detection of multiple targets. The book examines the methods and problems from a modeling perspective and surveys the state of current research on each topic and provides direction for further research exploration of the area.