*Generalized Linear, Mixed Effects and Nonparametric Regression Models*

Author: Julian J. Faraway

Publisher: CRC Press

ISBN: 9780203492284

Category: Mathematics

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## Extending the Linear Model with R

Linear models are central to the practice of statistics and form the foundation of a vast range of statistical methodologies. Julian J. Faraway's critically acclaimed Linear Models with R examined regression and analysis of variance, demonstrated the different methods available, and showed in which situations each one applies. Following in those footsteps, Extending the Linear Model with R surveys the techniques that grow from the regression model, presenting three extensions to that framework: generalized linear models (GLMs), mixed effect models, and nonparametric regression models. The author's treatment is thoroughly modern and covers topics that include GLM diagnostics, generalized linear mixed models, trees, and even the use of neural networks in statistics. To demonstrate the interplay of theory and practice, throughout the book the author weaves the use of the R software environment to analyze the data of real examples, providing all of the R commands necessary to reproduce the analyses. All of the data described in the book is available at http://people.bath.ac.uk/jjf23/ELM/ Statisticians need to be familiar with a broad range of ideas and techniques. This book provides a well-stocked toolbox of methodologies, and with its unique presentation of these very modern statistical techniques, holds the potential to break new ground in the way graduate-level courses in this area are taught.
## Linear Models with R, Second Edition

A Hands-On Way to Learning Data Analysis Part of the core of statistics, linear models are used to make predictions and explain the relationship between the response and the predictors. Understanding linear models is crucial to a broader competence in the practice of statistics. Linear Models with R, Second Edition explains how to use linear models in physical science, engineering, social science, and business applications. The book incorporates several improvements that reflect how the world of R has greatly expanded since the publication of the first edition. New to the Second Edition Reorganized material on interpreting linear models, which distinguishes the main applications of prediction and explanation and introduces elementary notions of causality Additional topics, including QR decomposition, splines, additive models, Lasso, multiple imputation, and false discovery rates Extensive use of the ggplot2 graphics package in addition to base graphics Like its widely praised, best-selling predecessor, this edition combines statistics and R to seamlessly give a coherent exposition of the practice of linear modeling. The text offers up-to-date insight on essential data analysis topics, from estimation, inference, and prediction to missing data, factorial models, and block designs. Numerous examples illustrate how to apply the different methods using R.
## Extending the Linear Model with R

Start Analyzing a Wide Range of Problems Since the publication of the bestselling, highly recommended first edition, R has considerably expanded both in popularity and in the number of packages available. Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models, Second Edition takes advantage of the greater functionality now available in R and substantially revises and adds several topics. New to the Second Edition Expanded coverage of binary and binomial responses, including proportion responses, quasibinomial and beta regression, and applied considerations regarding these models New sections on Poisson models with dispersion, zero inflated count models, linear discriminant analysis, and sandwich and robust estimation for generalized linear models (GLMs) Revised chapters on random effects and repeated measures that reflect changes in the lme4 package and show how to perform hypothesis testing for the models using other methods New chapter on the Bayesian analysis of mixed effect models that illustrates the use of STAN and presents the approximation method of INLA Revised chapter on generalized linear mixed models to reflect the much richer choice of fitting software now available Updated coverage of splines and confidence bands in the chapter on nonparametric regression New material on random forests for regression and classification Revamped R code throughout, particularly the many plots using the ggplot2 package Revised and expanded exercises with solutions now included Demonstrates the Interplay of Theory and Practice This textbook continues to cover a range of techniques that grow from the linear regression model. It presents three extensions to the linear framework: GLMs, mixed effect models, and nonparametric regression models. The book explains data analysis using real examples and includes all the R commands necessary to reproduce the analyses.
## Generalized Linear Mixed Models

Generalized Linear Mixed Models: Modern Concepts, Methods and Applications presents an introduction to linear modeling using the generalized linear mixed model (GLMM) as an overarching conceptual framework. For readers new to linear models, the book helps them see the big picture. It shows how linear models fit with the rest of the core statistics curriculum and points out the major issues that statistical modelers must consider. Along with describing common applications of GLMMs, the text introduces the essential theory and main methodology associated with linear models that accommodate random model effects and non-Gaussian data. Unlike traditional linear model textbooks that focus on normally distributed data, this one adopts a generalized mixed model approach throughout: data for linear modeling need not be normally distributed and effects may be fixed or random. With numerous examples using SAS® PROC GLIMMIX, this book is ideal for graduate students in statistics, statistics professionals seeking to update their knowledge, and researchers new to the generalized linear model thought process. It focuses on data-driven processes and provides context for extending traditional linear model thinking to generalized linear mixed modeling. See Professor Stroup discuss the book.
## Introduction to General and Generalized Linear Models

Bridging the gap between theory and practice for modern statistical model building, Introduction to General and Generalized Linear Models presents likelihood-based techniques for statistical modelling using various types of data. Implementations using R are provided throughout the text, although other software packages are also discussed. Numerous examples show how the problems are solved with R. After describing the necessary likelihood theory, the book covers both general and generalized linear models using the same likelihood-based methods. It presents the corresponding/parallel results for the general linear models first, since they are easier to understand and often more well known. The authors then explore random effects and mixed effects in a Gaussian context. They also introduce non-Gaussian hierarchical models that are members of the exponential family of distributions. Each chapter contains examples and guidelines for solving the problems via R. Providing a flexible framework for data analysis and model building, this text focuses on the statistical methods and models that can help predict the expected value of an outcome, dependent, or response variable. It offers a sound introduction to general and generalized linear models using the popular and powerful likelihood techniques. Ancillary materials are available at www.imm.dtu.dk/~hm/GLM
## A Modern Approach to Regression with R

This book focuses on tools and techniques for building regression models using real-world data and assessing their validity. A key theme throughout the book is that it makes sense to base inferences or conclusions only on valid models. Plots are shown to be an important tool for both building regression models and assessing their validity. We shall see that deciding what to plot and how each plot should be interpreted will be a major challenge. In order to overcome this challenge we shall need to understand the mathematical properties of the fitted regression models and associated diagnostic procedures. As such this will be an area of focus throughout the book. In particular, we shall carefully study the properties of resi- als in order to understand when patterns in residual plots provide direct information about model misspecification and when they do not. The regression output and plots that appear throughout the book have been gen- ated using R. The output from R that appears in this book has been edited in minor ways. On the book web site you will find the R code used in each example in the text.
## An R Companion to Linear Statistical Models

Focusing on user-developed programming, An R Companion to Linear Statistical Models serves two audiences: those who are familiar with the theory and applications of linear statistical models and wish to learn or enhance their skills in R; and those who are enrolled in an R-based course on regression and analysis of variance. For those who have never used R, the book begins with a self-contained introduction to R that lays the foundation for later chapters. This book includes extensive and carefully explained examples of how to write programs using the R programming language. These examples cover methods used for linear regression and designed experiments with up to two fixed-effects factors, including blocking variables and covariates. It also demonstrates applications of several pre-packaged functions for complex computational procedures.
## Statistical Theory

Designed for a one-semester advanced undergraduate or graduate course, Statistical Theory: A Concise Introduction clearly explains the underlying ideas and principles of major statistical concepts, including parameter estimation, confidence intervals, hypothesis testing, asymptotic analysis, Bayesian inference, and elements of decision theory. It introduces these topics on a clear intuitive level using illustrative examples in addition to the formal definitions, theorems, and proofs. Based on the authors’ lecture notes, this student-oriented, self-contained book maintains a proper balance between the clarity and rigor of exposition. In a few cases, the authors present a "sketched" version of a proof, explaining its main ideas rather than giving detailed technical mathematical and probabilistic arguments. Chapters and sections marked by asterisks contain more advanced topics and may be omitted. A special chapter on linear models shows how the main theoretical concepts can be applied to the well-known and frequently used statistical tool of linear regression. Requiring no heavy calculus, simple questions throughout the text help students check their understanding of the material. Each chapter also includes a set of exercises that range in level of difficulty.
## Linear Mixed-Effects Models Using R

Linear mixed-effects models (LMMs) are an important class of statistical models that can be used to analyze correlated data. Such data are encountered in a variety of fields including biostatistics, public health, psychometrics, educational measurement, and sociology. This book aims to support a wide range of uses for the models by applied researchers in those and other fields by providing state-of-the-art descriptions of the implementation of LMMs in R. To help readers to get familiar with the features of the models and the details of carrying them out in R, the book includes a review of the most important theoretical concepts of the models. The presentation connects theory, software and applications. It is built up incrementally, starting with a summary of the concepts underlying simpler classes of linear models like the classical regression model, and carrying them forward to LMMs. A similar step-by-step approach is used to describe the R tools for LMMs. All the classes of linear models presented in the book are illustrated using real-life data. The book also introduces several novel R tools for LMMs, including new class of variance-covariance structure for random-effects, methods for influence diagnostics and for power calculations. They are included into an R package that should assist the readers in applying these and other methods presented in this text.
## Statistical and Computational Methods in Brain Image Analysis

The massive amount of nonstandard high-dimensional brain imaging data being generated is often difficult to analyze using current techniques. This challenge in brain image analysis requires new computational approaches and solutions. But none of the research papers or books in the field describe the quantitative techniques with detailed illustrations of actual imaging data and computer codes. Using MATLAB® and case study data sets, Statistical and Computational Methods in Brain Image Analysis is the first book to explicitly explain how to perform statistical analysis on brain imaging data. The book focuses on methodological issues in analyzing structural brain imaging modalities such as MRI and DTI. Real imaging applications and examples elucidate the concepts and methods. In addition, most of the brain imaging data sets and MATLAB codes are available on the author’s website. By supplying the data and codes, this book enables researchers to start their statistical analyses immediately. Also suitable for graduate students, it provides an understanding of the various statistical and computational methodologies used in the field as well as important and technically challenging topics.
## Nonparametric and Semiparametric Models

The statistical and mathematical principles of smoothing with a focus on applicable techniques are presented in this book. It naturally splits into two parts: The first part is intended for undergraduate students majoring in mathematics, statistics, econometrics or biometrics whereas the second part is intended to be used by master and PhD students or researchers. The material is easy to accomplish since the e-book character of the text gives a maximum of flexibility in learning (and teaching) intensity.
## Generalized Linear Models, Second Edition

The success of the first edition of Generalized Linear Models led to the updated Second Edition, which continues to provide a definitive unified, treatment of methods for the analysis of diverse types of data. Today, it remains popular for its clarity, richness of content and direct relevance to agricultural, biological, health, engineering, and other applications. The authors focus on examining the way a response variable depends on a combination of explanatory variables, treatment, and classification variables. They give particular emphasis to the important case where the dependence occurs through some unknown, linear combination of the explanatory variables. The Second Edition includes topics added to the core of the first edition, including conditional and marginal likelihood methods, estimating equations, and models for dispersion effects and components of dispersion. The discussion of other topics-log-linear and related models, log odds-ratio regression models, multinomial response models, inverse linear and related models, quasi-likelihood functions, and model checking-was expanded and incorporates significant revisions. Comprehension of the material requires simply a knowledge of matrix theory and the basic ideas of probability theory, but for the most part, the book is self-contained. Therefore, with its worked examples, plentiful exercises, and topics of direct use to researchers in many disciplines, Generalized Linear Models serves as ideal text, self-study guide, and reference.
## An Introduction to Generalized Linear Models Fourth Edition

An Introduction to Generalized Linear Models, Fourth Edition provides a cohesive framework for statistical modelling, with an emphasis on numerical and graphical methods. This new edition of a bestseller has been updated with new sections on non-linear associations, strategies for model selection, and a Postface on good statistical practice. Like its predecessor, this edition presents the theoretical background of generalized linear models (GLMs) before focusing on methods for analyzing particular kinds of data. It covers Normal, Poisson, and Binomial distributions; linear regression models; classical estimation and model fitting methods; and frequentist methods of statistical inference. After forming this foundation, the authors explore multiple linear regression, analysis of variance (ANOVA), logistic regression, log-linear models, survival analysis, multilevel modeling, Bayesian models, and Markov chain Monte Carlo (MCMC) methods. Introduces GLMs in a way that enables readers to understand the unifying structure that underpins them Discusses common concepts and principles of advanced GLMs, including nominal and ordinal regression, survival analysis, non-linear associations and longitudinal analysis Connects Bayesian analysis and MCMC methods to fit GLMs Contains numerous examples from business, medicine, engineering, and the social sciences Provides the example code for R, Stata, and WinBUGS to encourage implementation of the methods Offers the data sets and solutions to the exercises online Describes the components of good statistical practice to improve scientific validity and reproducibility of results. Using popular statistical software programs, this concise and accessible text illustrates practical approaches to estimation, model fitting, and model comparisons.
## Generalized Additive Models

The first edition of this book has established itself as one of the leading references on generalized additive models (GAMs), and the only book on the topic to be introductory in nature with a wealth of practical examples and software implementation. It is self-contained, providing the necessary background in linear models, linear mixed models, and generalized linear models (GLMs), before presenting a balanced treatment of the theory and applications of GAMs and related models. The author bases his approach on a framework of penalized regression splines, and while firmly focused on the practical aspects of GAMs, discussions include fairly full explanations of the theory underlying the methods. Use of R software helps explain the theory and illustrates the practical application of the methodology. Each chapter contains an extensive set of exercises, with solutions in an appendix or in the book’s R data package gamair, to enable use as a course text or for self-study. Simon N. Wood is a professor of Statistical Science at the University of Bristol, UK, and author of the R package mgcv.
## Data Analysis Using Hierarchical Generalized Linear Models with R

Since their introduction, hierarchical generalized linear models (HGLMs) have proven useful in various fields by allowing random effects in regression models. Interest in the topic has grown, and various practical analytical tools have been developed. This book summarizes developments within the field and, using data examples, illustrates how to analyse various kinds of data using R. It provides a likelihood approach to advanced statistical modelling including generalized linear models with random effects, survival analysis and frailty models, multivariate HGLMs, factor and structural equation models, robust modelling of random effects, models including penalty and variable selection and hypothesis testing. This example-driven book is aimed primarily at researchers and graduate students, who wish to perform data modelling beyond the frequentist framework, and especially for those searching for a bridge between Bayesian and frequentist statistics.
## Flexible Regression and Smoothing

This book is about learning from data using the Generalized Additive Models for Location, Scale and Shape (GAMLSS). GAMLSS extends the Generalized Linear Models (GLMs) and Generalized Additive Models (GAMs) to accommodate large complex datasets, which are increasingly prevalent. GAMLSS allows any parametric distribution for the response variable and modelling all the parameters (location, scale and shape) of the distribution as linear or smooth functions of explanatory variables. This book provides a broad overview of GAMLSS methodology and how it is implemented in R. It includes a comprehensive collection of real data examples, integrated code, and figures to illustrate the methods, and is supplemented by a website with code, data and additional materials.
## Linear Models and the Relevant Distributions and Matrix Algebra

Linear Models and the Relevant Distributions and Matrix Algebra provides in-depth and detailed coverage of the use of linear statistical models as a basis for parametric and predictive inference. It can be a valuable reference, a primary or secondary text in a graduate-level course on linear models, or a resource used (in a course on mathematical statistics) to illustrate various theoretical concepts in the context of a relatively complex setting of great practical importance. Features: Provides coverage of matrix algebra that is extensive and relatively self-contained and does so in a meaningful context Provides thorough coverage of the relevant statistical distributions, including spherically and elliptically symmetric distributions Includes extensive coverage of multiple-comparison procedures (and of simultaneous confidence intervals), including procedures for controlling the k-FWER and the FDR Provides thorough coverage (complete with detailed and highly accessible proofs) of results on the properties of various linear-model procedures, including those of least squares estimators and those of the F test. Features the use of real data sets for illustrative purposes Includes many exercises David Harville served for 10 years as a mathematical statistician in the Applied Mathematics Research Laboratory of the Aerospace Research Laboratories at Wright-Patterson AFB, Ohio, 20 years as a full professor in Iowa State University’s Department of Statistics where he now has emeritus status, and seven years as a research staff member of the Mathematical Sciences Department of IBM’s T.J. Watson Research Center. He has considerable relevant experience, having taught M.S. and Ph.D. level courses in linear models, been the thesis advisor of 10 Ph.D. graduates, and authored or co-authored two books and more than 80 research articles. His work has been recognized through his election as a Fellow of the American Statistical Association and of the Institute of Mathematical Statistics and as a member of the International Statistical Institute.
## Plane Answers to Complex Questions

The second edition of Plane Answers has many additions and a couple of deletions. New material includes additional illustrative examples in Ap pendices A and B and Chapters 2 and 3, as well as discussions of Bayesian estimation, near replicate lack of fit tests, testing the independence assump tion, testing variance components, the interblock analysis for balanced in complete block designs, nonestimable constraints, analysis of unreplicated experiments using normal plots, tensors, and properties of Kronecker prod ucts and Vee operators. The book contains an improved discussion of the relation between ANOVA and regression, and an improved presentation of general Gauss-Markov models. The primary material that has been deleted are the discussions of weighted means and of log-linear models. The mate rial on log-linear models was included in Christensen (1990b), so it became redundant here. Generally, I have tried to clean up the presentation of ideas wherever it seemed obscure to me. Much of the work on the second edition was done while on sabbatical at the University of Canterbury in Christchurch, New Zealand. I would par ticularly like to thank John Deely for arranging my sabbatical. Through their comments and criticisms, four people were particularly helpful in con structing this new edition. I would like to thank Wes Johnson, Snehalata Huzurbazar, Ron Butler, and Vance Berger.
## The R Book

Hugely successful and popular text presenting an extensive and comprehensive guide for all R users The R language is recognized as one of the most powerful and flexible statistical software packages, enabling users to apply many statistical techniques that would be impossible without such software to help implement such large data sets. R has become an essential tool for understanding and carrying out research. This edition: Features full colour text and extensive graphics throughout. Introduces a clear structure with numbered section headings to help readers locate information more efficiently. Looks at the evolution of R over the past five years. Features a new chapter on Bayesian Analysis and Meta-Analysis. Presents a fully revised and updated bibliography and reference section. Is supported by an accompanying website allowing examples from the text to be run by the user. Praise for the first edition: ‘…if you are an R user or wannabe R user, this text is the one that should be on your shelf. The breadth of topics covered is unsurpassed when it comes to texts on data analysis in R.’ (The American Statistician, August 2008) ‘The High-level software language of R is setting standards in quantitative analysis. And now anybody can get to grips with it thanks to The R Book…’ (Professional Pensions, July 2007)
## Generalized Linear Models for Insurance Data

This is the only book actuaries need to understand generalized linear models (GLMs) for insurance applications. GLMs are used in the insurance industry to support critical decisions. Until now, no text has introduced GLMs in this context or addressed the problems specific to insurance data. Using insurance data sets, this practical, rigorous book treats GLMs, covers all standard exponential family distributions, extends the methodology to correlated data structures, and discusses recent developments which go beyond the GLM. The issues in the book are specific to insurance data, such as model selection in the presence of large data sets and the handling of varying exposure times. Exercises and data-based practicals help readers to consolidate their skills, with solutions and data sets given on the companion website. Although the book is package-independent, SAS code and output examples feature in an appendix and on the website. In addition, R code and output for all the examples are provided on the website.

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