Mixed Effects Models for Complex Data


Book Description

Although standard mixed effects models are useful in a range of studies, other approaches must often be used in correlation with them when studying complex or incomplete data. Mixed Effects Models for Complex Data discusses commonly used mixed effects models and presents appropriate approaches to address dropouts, missing data, measurement errors, censoring, and outliers. For each class of mixed effects model, the author reviews the corresponding class of regression model for cross-sectional data. An overview of general models and methods, along with motivating examples After presenting real data examples and outlining general approaches to the analysis of longitudinal/clustered data and incomplete data, the book introduces linear mixed effects (LME) models, generalized linear mixed models (GLMMs), nonlinear mixed effects (NLME) models, and semiparametric and nonparametric mixed effects models. It also includes general approaches for the analysis of complex data with missing values, measurement errors, censoring, and outliers. Self-contained coverage of specific topics Subsequent chapters delve more deeply into missing data problems, covariate measurement errors, and censored responses in mixed effects models. Focusing on incomplete data, the book also covers survival and frailty models, joint models of survival and longitudinal data, robust methods for mixed effects models, marginal generalized estimating equation (GEE) models for longitudinal or clustered data, and Bayesian methods for mixed effects models. Background material In the appendix, the author provides background information, such as likelihood theory, the Gibbs sampler, rejection and importance sampling methods, numerical integration methods, optimization methods, bootstrap, and matrix algebra. Failure to properly address missing data, measurement errors, and other issues in statistical analyses can lead to severely biased or misleading results. This book explores the biases that arise when naïve methods are used and shows which approaches should be used to achieve accurate results in longitudinal data analysis.




Bringing Bayesian Models to Life


Book Description

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.




Handbook of Bayesian Variable Selection


Book Description

Bayesian variable selection has experienced substantial developments over the past 30 years with the proliferation of large data sets. Identifying relevant variables to include in a model allows simpler interpretation, avoids overfitting and multicollinearity, and can provide insights into the mechanisms underlying an observed phenomenon. Variable selection is especially important when the number of potential predictors is substantially larger than the sample size and sparsity can reasonably be assumed. The Handbook of Bayesian Variable Selection provides a comprehensive review of theoretical, methodological and computational aspects of Bayesian methods for variable selection. The topics covered include spike-and-slab priors, continuous shrinkage priors, Bayes factors, Bayesian model averaging, partitioning methods, as well as variable selection in decision trees and edge selection in graphical models. The handbook targets graduate students and established researchers who seek to understand the latest developments in the field. It also provides a valuable reference for all interested in applying existing methods and/or pursuing methodological extensions. Features: Provides a comprehensive review of methods and applications of Bayesian variable selection. Divided into four parts: Spike-and-Slab Priors; Continuous Shrinkage Priors; Extensions to various Modeling; Other Approaches to Bayesian Variable Selection. Covers theoretical and methodological aspects, as well as worked out examples with R code provided in the online supplement. Includes contributions by experts in the field. Supported by a website with code, data, and other supplementary material




Spatial Capture-Recapture


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




Highly Structured Stochastic Systems


Book Description

Through this text, the author aims to make recent developments in the title subject (a modern strategy for the creation of statistical models to solve 'real world' problems) accessible to graduate students and researchers in the field of statistics.




Advanced Spatial Modeling with Stochastic Partial Differential Equations Using R and INLA


Book Description

Modeling spatial and spatio-temporal continuous processes is an important and challenging problem in spatial statistics. Advanced Spatial Modeling with Stochastic Partial Differential Equations Using R and INLA describes in detail the stochastic partial differential equations (SPDE) approach for modeling continuous spatial processes with a Matérn covariance, which has been implemented using the integrated nested Laplace approximation (INLA) in the R-INLA package. Key concepts about modeling spatial processes and the SPDE approach are explained with examples using simulated data and real applications. This book has been authored by leading experts in spatial statistics, including the main developers of the INLA and SPDE methodologies and the R-INLA package. It also includes a wide range of applications: * Spatial and spatio-temporal models for continuous outcomes * Analysis of spatial and spatio-temporal point patterns * Coregionalization spatial and spatio-temporal models * Measurement error spatial models * Modeling preferential sampling * Spatial and spatio-temporal models with physical barriers * Survival analysis with spatial effects * Dynamic space-time regression * Spatial and spatio-temporal models for extremes * Hurdle models with spatial effects * Penalized Complexity priors for spatial models All the examples in the book are fully reproducible. Further information about this book, as well as the R code and datasets used, is available from the book website at http://www.r-inla.org/spde-book. The tools described in this book will be useful to researchers in many fields such as biostatistics, spatial statistics, environmental sciences, epidemiology, ecology and others. Graduate and Ph.D. students will also find this book and associated files a valuable resource to learn INLA and the SPDE approach for spatial modeling.




A First Course in Bayesian Statistical Methods


Book Description

A self-contained introduction to probability, exchangeability and Bayes’ rule provides a theoretical understanding of the applied material. Numerous examples with R-code that can be run "as-is" allow the reader to perform the data analyses themselves. The development of Monte Carlo and Markov chain Monte Carlo methods in the context of data analysis examples provides motivation for these computational methods.




Mixed Models


Book Description

Praise for the First Edition “This book will serve to greatly complement the growing number of texts dealing with mixed models, and I highly recommend including it in one’s personal library.” —Journal of the American Statistical Association Mixed modeling is a crucial area of statistics, enabling the analysis of clustered and longitudinal data. Mixed Models: Theory and Applications with R, Second Edition fills a gap in existing literature between mathematical and applied statistical books by presenting a powerful examination of mixed model theory and application with special attention given to the implementation in R. The new edition provides in-depth mathematical coverage of mixed models’ statistical properties and numerical algorithms, as well as nontraditional applications, such as regrowth curves, shapes, and images. The book features the latest topics in statistics including modeling of complex clustered or longitudinal data, modeling data with multiple sources of variation, modeling biological variety and heterogeneity, Healthy Akaike Information Criterion (HAIC), parameter multidimensionality, and statistics of image processing. Mixed Models: Theory and Applications with R, Second Edition features unique applications of mixed model methodology, as well as: Comprehensive theoretical discussions illustrated by examples and figures Over 300 exercises, end-of-section problems, updated data sets, and R subroutines Problems and extended projects requiring simulations in R intended to reinforce material Summaries of major results and general points of discussion at the end of each chapter Open problems in mixed modeling methodology, which can be used as the basis for research or PhD dissertations Ideal for graduate-level courses in mixed statistical modeling, the book is also an excellent reference for professionals in a range of fields, including cancer research, computer science, and engineering.




Linear Mixed-Effects Models Using R


Book Description

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.




Bayesian inference with INLA


Book Description

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.