Mixture And Hidden Markov Models With R

This book discusses mixture and hidden Markov models for modeling behavioral data. Mixture and hidden Markov models are statistical models which are useful when an observed system occupies a number of distinct “regimes” or unobserved (hidden) states. These models are widely used in a variety of fields, including artificial intelligence, biology, finance, and psychology. Hidden Markov models can be viewed as an extension of mixture models, to model transitions between states over time. Covering both mixture and hidden Markov models in a single book allows main concepts and issues to be introduced in the relatively simpler context of mixture models. After a thorough treatment of the theory and practice of mixture modeling, the conceptual leap towards hidden Markov models is relatively straightforward. This book provides many practical examples illustrating the wide variety of uses of the models. These examples are drawn from our own work in psychology, as well as other areas such as financial time series and climate data. Most examples illustrate the use of the authors’ depmixS4 package, which provides a flexible framework to construct and estimate mixture and hidden Markov models. All examples are fully reproducible and the accompanying hmmR package provides all the datasets used, as well as additional functionality. This book is suitable for advanced students and researchers with an applied background.

Hidden Markov Models for Time Series: An Introduction Using R, Second Edition illustrates the great flexibility of hidden Markov models (HMMs) as general-purpose models for time series data. The book provides a broad understanding of the models and their uses. After presenting the basic model formulation, the book covers estimation, forecasting, decoding, prediction, model selection, and Bayesian inference for HMMs. Through examples and applications, the authors describe how to extend and generalize the basic model so that it can be applied in a rich variety of situations. The book demonstrates how HMMs can be applied to a wide range of types of time series: continuous-valued, circular, multivariate, binary, bounded and unbounded counts, and categorical observations. It also discusses how to employ the freely available computing environment R to carry out the computations. Features Presents an accessible overview of HMMs Explores a variety of applications in ecology, finance, epidemiology, climatology, and sociology Includes numerous theoretical and programming exercises Provides most of the analysed data sets online New to the second edition A total of five chapters on extensions, including HMMs for longitudinal data, hidden semi-Markov models and models with continuous-valued state process New case studies on animal movement, rainfall occurrence and capture-recapture data

Reveals How HMMs Can Be Used as General-Purpose Time Series Models Implements all methods in R Hidden Markov Models for Time Series: An Introduction Using R applies hidden Markov models (HMMs) to a wide range of time series types, from continuous-valued, circular, and multivariate series to binary data, bounded and unbounded counts, and categorical observations. It also discusses how to employ the freely available computing environment R to carry out computations for parameter estimation, model selection and checking, decoding, and forecasting. Illustrates the methodology in action After presenting the simple Poisson HMM, the book covers estimation, forecasting, decoding, prediction, model selection, and Bayesian inference. Through examples and applications, the authors describe how to extend and generalize the basic model so it can be applied in a rich variety of situations. They also provide R code for some of the examples, enabling the use of the codes in similar applications. Effectively interpret data using HMMs This book illustrates the wonderful flexibility of HMMs as general-purpose models for time series data. It provides a broad understanding of the models and their uses.

The current volume, Advances in Latent Variable Mixture Models, contains chapters by all of the speakers who participated in the 2006 CILVR conference, providing not just a snapshot of the event, but more importantly chronicling the state of the art in latent variable mixture model research. The volume starts with an overview chapter by the CILVR conference keynote speaker, Bengt Muthén, offering a “lay of the land” for latent variable mixture models before the volume moves to more specific constellations of topics. Part I, Multilevel and Longitudinal Systems, deals with mixtures for data that are hierarchical in nature either due to the data’s sampling structure or to the repetition of measures (of varied types) over time. Part II, Models for Assessment and Diagnosis, addresses scenarios for making judgments about individuals’ state of knowledge or development, and about the instruments used for making such judgments. Finally, Part III, Challenges in Model Evaluation, focuses on some of the methodological issues associated with the selection of models most accurately representing the processes and populations under investigation. It should be stated that this volume is not intended to be a first exposure to latent variable methods. Readers lacking such foundational knowledge are encouraged to consult primary and/or secondary didactic resources in order to get the most from the chapters in this volume. Once armed with the basic understanding of latent variable methods, we believe readers will find this volume incredibly exciting.

Hidden Markov models (HMMs) and other latent variable models form complex, flexible frameworks for univariate and multivariate data structures. In the last two decades models with latent variables have entered almost all fields of statistical applications. It is common for these models that unobserved variables are introduced to model a complex data structure given by the observables. A major advantage of latent structures is the principle simplicity and the accessibility to practitioners as well as their application-driven interpretations rather than black box systems. In this dissertation the statistical methodology of HMMs and related models is extended in certain aspects and illustrated by several applications from various fields, including epileptic seizures, financial time series and a dental health trail. We first investigate testing problems for HMMs under nonstandard conditions, namely when the true parameter lies on the boundary. In practical applications of HMMs, non-standard testing problems are frequently encountered, e.g. testing for the probability of staying in a certain unobserved state being zero. We derive the relevant asymptotic distribution theory for the likelihood ratio test in HMMs under these conditions. A number of examples with particular relevance in the HMM framework are examined. Secondly, we are concerned with testing for the number of states in HMMs and switching regression models, in particular, testing for two states in an HMM, and testing for two components in switching regression models. The specification of the number of states is very important in all models with discrete latent variables, and performing statistical testing of such hypotheses is one way to deal with this problem. For testing for homogeneity or for two components in finite mixtures the modified likelihood ratio test is a well-developed method. Based on this approach we propose a test for two states in HMMs. Testing for two states is of primary interest in particular for HMMs, since a two-state HMM represents the smallest non-trivial member of this model class. We derive the asymptotic distribution for the modified likelihood ratio test with independence assumption under the hypothesis of a two-state HMM. In addition, we propose a test for two components in switching regression models with independent or Markov-dependent regime. In the third part we depart from the classical parametric framework and relax the parametric assumptions, aiming for more flexible models, which reduce systematic errors caused by model misspecification and give rise to model validation techniques. We propose a parametric as well as a semiparametric approach to this problem. In particular, the latter one introduces a new flavor to hidden Markov modeling by linking recently developed semiparametric mixture models to the HMM framework. We discuss identifiability and propose an estimation procedure to semiparametric two-state HMMs based on the expectation-maximization algorithm. This enables extensions of modern estimation techniques in semiparametric mixtures like log-concave density estimation to HMMs.

This open access book provides innovative methods and original applications of sequence analysis (SA) and related methods for analysing longitudinal data describing life trajectories such as professional careers, family paths, the succession of health statuses, or the time use. The applications as well as the methodological contributions proposed in this book pay special attention to the combined use of SA and other methods for longitudinal data such as event history analysis, Markov modelling, and sequence network. The methodological contributions in this book include among others original propositions for measuring the precarity of work trajectories, Markov-based methods for clustering sequences, fuzzy and monothetic clustering of sequences, network-based SA, joint use of SA and hidden Markov models, and of SA and survival models. The applications cover the comparison of gendered occupational trajectories in Germany, the study of the changes in women market participation in Denmark, the study of typical day of dual-earner couples in Italy, of mobility patterns in Togo, of internet addiction in Switzerland, and of the quality of employment career after a first unemployment spell. As such this book provides a wealth of information for social scientists interested in quantitative life course analysis, and all those working in sociology, demography, economics, health, psychology, social policy, and statistics.; Provides new perspectives and methods for sequence analysis Focusses on the link between sequence analysis and other methods for longitudinal data, especially event history analysis and Markov models Stresses the complementarity of sequence analysis and other models for longitudinal data Applications of sequence analysis in a whole range of different domains This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

This volume reviews longitudinal models and analysis procedures for use in the behavioral and social sciences. Written by distinguished experts in the field, the book presents the most current approaches and theories, and the technical problems that may be encountered along the way. Readers will find new ideas about the use of longitudinal analysis in solving problems that arise due to the specific nature of the research design and the data available. Longitudinal Models in the Behavioral and Related Sciences opens with the latest theoretical developments. In particular, the book addresses situations that arise due to the categorical nature of the data, issues related to state space modeling, and potential problems that may arise from network analysis and/or growth-curve data. The focus of part two is on the application of longitudinal modeling in a variety of disciplines. The book features applications such as heterogeneity on the patterns of a firm’s profit, on house prices, and on delinquent behavior; non-linearity in growth in assessing cognitive aging; measurement error issues in longitudinal research; and distance association for the analysis of change. Part two clearly demonstrates the caution that should be taken when applying longitudinal modeling as well as in the interpretation of the results. This new volume is ideal for advanced students and researchers in psychology, sociology, education, economics, management, medicine, and neuroscience.

The past decade has seen powerful new computational tools for modeling which combine a Bayesian approach with recent Monte simulation techniques based on Markov chains. This book is the first to offer a systematic presentation of the Bayesian perspective of finite mixture modelling. The book is designed to show finite mixture and Markov switching models are formulated, what structures they imply on the data, their potential uses, and how they are estimated. Presenting its concepts informally without sacrificing mathematical correctness, it will serve a wide readership including statisticians as well as biologists, economists, engineers, financial and market researchers.