R in a Nutshell: A Desktop Quick Reference Review

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(More customer reviews)'R in a Nutshell' is the essential introductory book on R. Do not try to learn R without it.
I made two attempts to learn R before purchasing this book. In both previous attempts, I had to abort and use another tool to solve my problem because it was taking me too long to accomplish very simple things in R.
The reason R is hard to learn is that its documentation is organized for statisticians that already know R, but have forgotten a detail or two. There are a few other books on learning R, but they are setup like a college course - complete the entire book and THEN you can actually accomplish something.
R in a Nutshell allows you to get working immediately. Simply lookup what you need to do. The firsts thing I did was load a file and make a histogram. I found that stuff in the section on "Loading Data" and the section on charts. In no time I was making stacked area charts for cohorts. Now R is an essential tool for me - and I haven't even taken the time to learn it well! With this book, I don't have to. I can learn as I go. So I actually use R.
Do not R without it.

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What people are saying about R in a Nutshell

"I am excited about this book. R in a Nutshell is a great introduction to R, as well as a comprehensive reference for using R in data analytics and visualization. Adler provides 'real world' examples, practical advice, and scripts, making it accessible to anyone working with data, not just professional statisticians." --Martin Schultz, Arthur K. Watson Professor of Computer Science, Yale University

"R in a Nutshell is an ideal book for getting started with R. Newcomers will find the fundamentals for performing statistical analysis and graphics, all illustrated with practical examples. This book is an invaluable reference for anyone who wants to learn what R is and what is can do, even for longtime R users looking for new tips and tricks." --David M. Smith, Editor of the "Revolutions" blog at REvolution Computing

Why learn R? Because it's rapidly becoming the standard for developing statistical software. R in a Nutshell provides a quick and practical way to learn this increasingly popular open source language and environment. You'll not only learn how to program in R, but also how to find the right user-contributed R packages for statistical modeling, visualization, and bioinformatics.

The author introduces you to the R environment, including the R graphical user interface and console, and takes you through the fundamentals of the object-oriented R language. Then, through a variety of practical examples from medicine, business, and sports, you'll learn how you can use this remarkable tool to solve your own data analysis problems.

Understand the basics of the language, including the nature of R objects
Learn how to write R functions and build your own packages
Work with data through visualization, statistical analysis, and other methods
Explore the wealth of packages contributed by the R community
Become familiar with the lattice graphics package for high-level data visualization
Learn about bioinformatics packages provided by Bioconductor

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Temporal Data Mining (Chapman & Hall/CRC Data Mining and Knowledge Discovery Series) Review

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(More customer reviews)A survey of remarkable breadth, listing hundreds of sources: 50-100 items per chapter, majority of them from conference proceedings. Evidently, this kind of volume does not let the author discuss any particular paper or topic in detail; at best, a reference is covered with a short paragraph. This does create a problem: the book's value is exhausted once the reader looks up the topic of interest, and moves on to the suggested references. "Temporal data mining" could do with a little more editing, but I am quite impressed with it the way it is, an authoritative and wide-ranging introduction to an interesting topic.

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Temporal data mining deals with the harvesting of useful information from temporal data. New initiatives in health care and business organizations have increased the importance of temporal information in data today.From basic data mining concepts to state-of-the-art advances, Temporal Data Mining covers the theory of this subject as well as its application in a variety of fields. It discusses the incorporation of temporality in databases as well as temporal data representation, similarity computation, data classification, clustering, pattern discovery, and prediction. The book also explores the use of temporal data mining in medicine and biomedical informatics, business and industrial applications, web usage mining, and spatiotemporal data mining.Along with various state-of-the-art algorithms, each chapter includes detailed references and short descriptions of relevant algorithms and techniques described in other references. In the appendices, the author explains how data mining fits the overall goal of an organization and how these data can be interpreted for the purpose of characterizing a population. She also provides programs written in the Java language that implement some of the algorithms presented in the first chapter. Check out the author's blog at http://theophanomitsa.wordpress.com/

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A Primer of Ecology with R (Use R) Review

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(More customer reviews)This primer provides an excellent, upper-level, introduction to theoretical and simulation ecology. Working through the presented R code and exercises provides a deeper understanding of the thinking of many of the most famous theoretical ecologists, while also introducing the methods by which students can examine ecological questions through simulation.

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Provides simple explanations of the important concepts in population and community ecology.Provides R code throughout, to illustrate model development and analysis, as well as appendix introducing the R language.Interweaves ecological content and code so that either stands alone. Supplemental web site for additional code.

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Multivariate Statistical Modelling Based on Generalized Linear Models (Springer Series in Statistics) Review

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(More customer reviews)Back in 2000 Stephen Fienberg gave a talk at the University of California at Irvine on the 2000 census and his book "Who Counts". After the talk I went to dinner with him, my colleague Bob Newcomb and Anita Iannucci. Driving to dinner Bob ask Steve for a recommendation on a multivariate textbook. A number of choice were mentioned. Bob's favorite was Cooley and Lohnes but that was a bit dated. He was definitely looking for an applied text and not a theoretical one. I learned my multivariate analysis out of the first edition of Ted Anderson's book. But that is traditional multivariate Gaussian theory and is not at all an applied text. I always liked Gnanadesikan's book and I mentioned that. Srivastava and carter is an applied text that I like and there are many other choices.
I don't recall many of Fienberg's suggestions but I do distinctly recall that he did say that now you can teach it as a special case of the generalized linear models. The idea seemed to make sense to me but I couldn't picture the details. This book is apparently the book Fienberg had in mind. He might have been thinking about the first edition because this second edition was not out then.
The book is very applied and modern and covers many important topics for biostatisticians. Coverage includes multicategorical responses, semi and nonparametric modelling, time series and longitudinal data, random effects models, state space models including Kalman Filters and nonlinear models, and survival analysis. This is not traditional multivariate data but covers many type of multivariate data and models that do not fit the standard multivariate Gaussian theory.
Chapter 4 on selecting and checking models seems to deal with the classical linear models taking a non-standard approach through the methods of generalized linear models.
Excellent text for an applied course and for a reference book. It also covers hidden Markov models and Bayesian methods (including the MCMC implementation and the WinBugs software).


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The book is aimed at applied statisticians, graduate students of statistics, and students and researchers with a strong interest in statistics and data analysis. This second edition is extensively revised, especially those sections relating with Bayesian concepts.

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Mixed Effects Models and Extensions in Ecology with R Review

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(More customer reviews)Many applications in ecology clearly are not amenable to use of the general linear model due to violations of its assumptions. In fact, in most projects I work on, things like correlation among the errors, nonconstant error variance, etc., are the rule, rather than the exception. If you are looking for an applied text dealing with these types of situations with lots of examples, and demonstrations on analysis in R, then you should get this book. It does not delve into theory; there are plenty of other textbooks where you can fill in those details if you are interested. Rather, this book would be ideally suited for quantitative ecologists, biometricians, and statistical consultants who work in life sciences. Another nice thing is that the book does not assume you are an "R expert". Well done.

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This book discusses advanced statistical methods that can be used to analyse ecological data. Most environmental collected data are measured repeatedly over time, or space and this requires the use of GLMM or GAMM methods. The book starts by revising regression, additive modelling, GAM and GLM, and then discusses dealing with spatial or temporal dependencies and nested data.

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Nonparametric Regression Methods for Longitudinal Data Analysis: Mixed-Effects Modeling Approaches (Wiley Series in Probability and Statistics) Review

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(More customer reviews)Very good introductory text for nonparametric regression. This book first gives motivation for the processes, outlines the methods of smoothing, and then covers various regression techniques. Not particularly mathematical, although some linear algebra knowledge is necessary. Very accessible as a first course. Does not go very in-depth into the theory of any of the methods, however.

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Incorporates mixed-effects modeling techniques for more powerful and efficient methodsThis book presents current and effective nonparametric regression techniques for longitudinal data analysis and systematically investigates the incorporation of mixed-effects modeling techniques into various nonparametric regression models. The authors emphasize modeling ideas and inference methodologies, although some theoretical results for the justification of the proposed methods are presented.With its logical structure and organization, beginning with basic principles, the text develops the foundation needed to master advanced principles and applications. Following a brief overview, data examples from biomedical research studies are presented and point to the need for nonparametric regression analysis approaches. Next, the authors review mixed-effects models and nonparametric regression models, which are the two key building blocks of the proposed modeling techniques.The core section of the book consists of four chapters dedicated to the major nonparametric regression methods: local polynomial, regression spline, smoothing spline, and penalized spline. The next two chapters extend these modeling techniques to semiparametric and time varying coefficient models for longitudinal data analysis. The final chapter examines discrete longitudinal data modeling and analysis.Each chapter concludes with a summary that highlights key points and also provides bibliographic notes that point to additional sources for further study. Examples of data analysis from biomedical research are used to illustrate the methodologies contained throughout the book. Technical proofs are presented in separate appendices.With its focus on solving problems, this is an excellent textbook for upper-level undergraduate and graduate courses in longitudinal data analysis. It is also recommended as a reference for biostatisticians and other theoretical and applied research statisticians with an interest in longitudinal data analysis. Not only do readers gain an understanding of the principles of various nonparametric regression methods, but they also gain a practical understanding of how to use the methods to tackle real-world problems.

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Cognitive Modeling Review

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(More customer reviews)This book is quite easy to follow and describes the technical and practical details how to actually do cognitive modeling!
Highly recommended for people who are interested in cognitive modeling but don't know where to start.

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Cognitive Modeling is the first book to provide students with an easy-to understand introduction to the basic methods used to build and test cognitive models. Authors Jerome R. Busemeyer and Adele Diederich answer many of the questions that researchers face when beginning work on cognitive models, such as the following: What makes a cognitive model different from conceptual or statistical models? How do you develop such a model? How can you derive qualitatively different predictions between two cognitive models? Focusing on a few key representations, the authors introduce a basic problem in each chapter, illustrate the concept with three examples, and end with a summary of general principles, making this book by far the most accessible cognitive modeling book on the market. Key Features

Emphasizes modeling by presenting the tools needed to build a cognitive model, rather than simply reviewing existing models of cognition
Provides tutorial presentations of psychological, mathematical, statistical, and computational methods used in all areas of cognitive modeling
Includes detailed examples applied to real cognitive models published in the literature in a variety of areas, including recognition, categorization, decision making, and learning
Stresses the importance of designing the right conditions for evaluating models
Addresses the issues of individual differences in cognitive modeling head-on

Cognitive Modeling is ideal for students and researchers across the various domains of cognitive sciences, including perception, learning, decision making, and inference. It is intended for use in upper-level undergraduate and graduate courses such as Cognition/Cognitive Modeling, Cognitive Science, Cognitive Psychology, Quantitative Methods, and Mathematical Modeling in Psychology.

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Introduction to Time Series Modeling (Chapman & Hall/CRC Monographs on Statistics & Applied Probability) Review

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(More customer reviews)Here is the table of contents from the CRC site.
Introduction and Preparatory Analysis
Time Series Data
Classification of Time Series
Objectives of Time Series Analysis
Preprocessing of Time Series
Organization of This Book
The Covariance Function
The Distribution of Time Series and Stationarity
The Autocovariance Function of Stationary Time Series
Estimation of the Autocovariance Function
Multivariate Time Series and Scatterplots
Cross-Covariance Function and Cross-Correlation Function
The Power Spectrum and the Periodogram
The Power Spectrum
The Periodogram
Averaging and Smoothing of the Periodogram
Computational Method of Periodogram
Computation of the Periodogram by Fast Fourier Transform
Statistical Modeling
Probability Distributions and Statistical Models
K-L Information and the Entropy Maximization Principle
Estimation of the K-L Information and Log-Likelihood
Estimation of Parameters by the Maximum Likelihood Method
Akaike Information Criterion (AIC)
Transformation of Data
The Least Squares Method
Regression Models and the Least Squares Method
Householder Transformation Method
Selection of Order by AIC
Addition of Data and Successive Householder Reduction
Variable Selection by AIC
Analysis of Time Series Using ARMA Models
ARMA Model
The Impulse Response Function
The Autocovariance Function
The Relation between AR Coefficients and the PARCOR
The Power Spectrum of the ARMA Process
The Characteristic Equation
The Multivariate AR Model
Estimation of an AR Model
Fitting an AR Model
Yule-Walker Method and Levinson's Algorithm
Estimation of an AR Model by the Least Squares Method
Estimation of an AR Model by the PARCOR Method
Large Sample Distribution of the Estimates
Yule-Walker Method for MAR Model
Least Squares Method for MAR Model
The Locally Stationary AR Model
Locally Stationary AR Model
Automatic Partitioning of the Time Interval
Precise Estimation of a Change Point
Analysis of Time Series with a State-Space Model
The State-Space Model
State Estimation via the Kalman Filter
Smoothing Algorithms
Increasing Horizon Prediction of the State
Prediction of Time Series
Likelihood Computation and Parameter Estimation for a Time Series Model
Interpolation of Missing Observations
Estimation of the ARMA Model
State-Space Representation of the ARMA Model
Initial State of an ARMA Model
Maximum Likelihood Estimate of an ARMA Model
Initial Estimates of Parameters
Estimation of Trends
The Polynomial Trend Model
Trend Component Model--Model for Probabilistic Structural Changes
Trend Model
The Seasonal Adjustment Model
Seasonal Component Model
Standard Seasonal Adjustment Model
Decomposition Including an AR Component
Decomposition Including a Trading-Day Effect
Time-Varying Coefficient AR Model
Time-Varying Variance Model
Time-Varying Coefficient AR Model
Estimation of the Time-Varying Spectrum
The Assumption on System Noise for the Time-Varying Coefficient AR Model
Abrupt Changes of Coefficients
Non-Gaussian State-Space Model
Necessity of Non-Gaussian Models
Non-Gaussian State-Space Models and State Estimation
Numerical Computation of the State Estimation Formula
Non-Gaussian Trend Model
A Time-Varying Variance Model
Applications of Non-Gaussian State-Space Model
The Sequential Monte Carlo Filter
The Nonlinear Non-Gaussian State-Space Model and Approximations of Distributions
Monte Carlo Filter
Monte Carlo Smoothing Method
Nonlinear Smoothing
Simulation
Generation of Uniform Random Numbers
Generation of Gaussian White Noise
Simulation Using a State-Space Model
Simulation with Non-Gaussian Model
Appendix A: Algorithms for Nonlinear Optimization
Appendix B: Derivation of Levinson's Algorithm
Appendix C: Derivation of the Kalman Filter and Smoother Algorithms
Appendix D: Algorithm for the Monte Carlo Filter
Bibliography

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In time series modeling, the behavior of a certain phenomenon is expressed in relation to the past values of itself and other covariates. Since many important phenomena in statistical analysis are actually time series and the identification of conditional distribution of the phenomenon is an essential part of the statistical modeling, it is very important and useful to learn fundamental methods of time series modeling. Illustrating how to build models for time series using basic methods, Introduction to Time Series Modeling covers numerous time series models and the various tools for handling them.The book employs the state-space model as a generic tool for time series modeling and presents convenient recursive filtering and smoothing methods, including the Kalman filter, the non-Gaussian filter, and the sequential Monte Carlo filter, for the state-space models. Taking a unified approach to model evaluation based on the entropy maximization principle advocated by Dr. Akaike, the author derives various methods of parameter estimation, such as the least squares method, the maximum likelihood method, recursive estimation for state-space models, and model selection by the Akaike information criterion (AIC). Along with simulation methods, he also covers standard stationary time series models, such as AR and ARMA models, as well as nonstationary time series models, including the locally stationary AR model, the trend model, the seasonal adjustment model, and the time-varying coefficient AR model.With a focus on the description, modeling, prediction, and signal extraction of times series, this book provides basic tools for analyzing time series that arise in real-world problems. It encourages readers to build models for their own real-life problems.

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Regression Modeling Strategies: With Applications to Linear Models, Logistic Regression, and Survival Analysis (Springer Series in Statistics) Review

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(More customer reviews)Frank Harrell is a Professor who does a lot of consulting in medical research. This book covers a wide variety of topics in regression analysis including many advanced techniques including data reduction, smoothing techniques, variable selection, transformations, shrinkage methods, tree-based methods and resampling. But note the title "Regression Modeling Strategies". Unlike most advanced texts in regression this book emphasizes modeling strategies. So the focus is on things like variable selection and other techniques to avoid overfitting models and diagnostics to look for violations in assumptions such as variance homogeneity or normality and independence of residuals, or stability problems like colinearity.
The book covers an extensive collection of modern techniques for exploratory data analysis. Inferential methods are also considered and he deals appropriately with important issues (particularly for medical research) such as imputation of missing values. Many examples are considered and illustrated in S-PLUS.
Harrell also provides many rules of thumb based on his own experience building models. A lot of the techniques are illustrated using data from the Titanic where it is interesting to see which factors affected the probability of survival. My only disappointment was that there is perhaps too much emphasis on this one particular data set.
A standard regression text would be expected to include linear and nonlinear regression. Harrell goes much deeper including nonparametric regression, logistic regression and survival models (e.g. the Cox proportional hazards model).


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Many texts are excellent sources of knowledge about individual statistical tools, but the art of data analysis is about choosing and using multiple tools. Instead of presenting isolated techniques, this text emphasizes problem solving strategies that address the many issues arising when developing multivariable models using real data and not standard textbook examples. It includes imputation methods for dealing with missing data effectively, methods for dealing with nonlinear relationships and for making the estimation of transformations a formal part of the modeling process, methods for dealing with "too many variables to analyze and not enough observations," and powerful model validation techniques based on the bootstrap. This text realistically deals with model uncertainty and its effects on inference to achieve "safe data mining".

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