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.

A Hands-On Way to Learning Data AnalysisPart 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

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 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.

A Primer on Linear Models presents a unified, thorough, and rigorous development of the theory behind the statistical methodology of regression and analysis of variance (ANOVA). It seamlessly incorporates these concepts using non-full-rank design matrices and emphasizes the exact, finite sample theory supporting common statistical methods.

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.

State space models have gained tremendous popularity in recent years in as disparate fields as engineering, economics, genetics and ecology. After a detailed introduction to general state space models, this book focuses on dynamic linear models, emphasizing their Bayesian analysis. Whenever possible it is shown how to compute estimates and forecasts in closed form; for more complex models, simulation techniques are used. A final chapter covers modern sequential Monte Carlo algorithms. The book illustrates all the fundamental steps needed to use dynamic linear models in practice, using R. Many detailed examples based on real data sets are provided to show how to set up a specific model, estimate its parameters, and use it for forecasting. All the code used in the book is available online. No prior knowledge of Bayesian statistics or time series analysis is required, although familiarity with basic statistics and R is assumed.

This book is about making machine learning models and their decisions interpretable. After exploring the concepts of interpretability, you will learn about simple, interpretable models such as decision trees, decision rules and linear regression. Later chapters focus on general model-agnostic methods for interpreting black box models like feature importance and accumulated local effects and explaining individual predictions with Shapley values and LIME. All interpretation methods are explained in depth and discussed critically. How do they work under the hood? What are their strengths and weaknesses? How can their outputs be interpreted? This book will enable you to select and correctly apply the interpretation method that is most suitable for your machine learning project.