R Cookbook (O'Reilly Cookbooks) Review

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(More customer reviews)I'd give this book ten stars if I could. I bought one copy for the office and one for my house. This guy has the ability to write simply and with the mind set of people who are busy and want to get results right away. Of course we'd all love to be leisurely scholars and plow through theory and practice but most of us just need to get things done. A good example is the way he treats ARIMA. He warns you about using auto.arima but does not hide it from you because it is "dangerous." The book is full of tips, well organized and is oriented towards beginners, though it gets into depth. So many of the R books I've read absolutely pound you with up front details, some of which relate to obscure concerns, rather than starting with a task. For example, on page 199 he writes "Problem -- you want to count the relative frequency of certain observations in your sample" Next is "Solution" -- and he explains just the minimum needed to do that job. Some of the tips are just simple time savers, such as the function head(dataframe) to show a few of the dataframe rows at the start and tail(dataframe) to show a few at the end. Finally .... I don't know this writer personally, but I hope he keeps on writing because it is a craft he has thoroughly absorbed somewhere along the line.Bill Yarberry, Houston, TX


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With more than 200 practical recipes, this book helps you perform data analysis with R quickly and efficiently. The R language provides everything you need to do statistical work, but its structure can be difficult to master. This collection of concise, task-oriented recipes makes you productive with R immediately, with solutions ranging from basic tasks to input and output, general statistics, graphics, and linear regression.

Each recipe addresses a specific problem, with a discussion that explains the solution and offers insight into how it works. If you're a beginner, R Cookbook will help get you started. If you're an experienced data programmer, it will jog your memory and expand your horizons. You'll get the job done faster and learn more about R in the process.

Create vectors, handle variables, and perform other basic functions
Input and output data
Tackle data structures such as matrices, lists, factors, and data frames
Work with probability, probability distributions, and random variables
Calculate statistics and confidence intervals, and perform statistical tests
Create a variety of graphic displays
Build statistical models with linear regressions and analysis of variance (ANOVA)
Explore advanced statistical techniques, such as finding clusters in your data

"Wonderfully readable, R Cookbook serves not only as a solutions manual of sorts, but as a truly enjoyable way to explore the R language—one practical example at a time." —Jeffrey Ryan, software consultant and R package author

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Econometric Analysis of Count Data Review

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(More customer reviews)excellent. the book provides good examples and helps the readers to relate the huge literature and how one paper is related to another one.

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The book provides an up-to-date survey of statistical and econometric techniques for the analysis of count data, with a focus on conditional distribution models. The book starts with a presentation of the benchmark Poisson regression model. Alternative models address unobserved heterogeneity, state dependence, selectivity, endogeneity, underreporting, and clustered sampling. Testing and estimation is discussed. Finally, applications are reviewed in various fields.

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Modelling and Quantitative Methods in Fisheries, Second Edition Review

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(More customer reviews)In my opinion, Malcolm Haddon has managed a "tour de force" with this book. He not only covered most of the modern methods of quantitative analysis and modelling in fisheries science but he did so in a clear and relatively simple language. His book is approachable to all biologists with a basic understanding of mathematics and statistics. Yet, he managed to cover both the theoretical underpinnings of the methods and the practical aspects of their use (options, pitfalls ... etc.). In addition, the book gives MS Excel examples of the methods which should allow those of us who are not programmers to fully appreciate the methods by using them interactively. The Excel spreadsheets are also available for download on two web sites.

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With numerous real-world examples, Modelling and Quantitative Methods in Fisheries, Second Edition provides an introduction to the analytical methods used by fisheries' scientists and ecologists. By following the examples using Excel, readers see the nuts and bolts of how the methods work and better understand the underlying principles. Excel workbooks are available for download from CRC Press Online.In this second edition, the author has revised all chapters and improved a number of the examples. This edition also includes two entirely new chapters:Characterization of Uncertainty covers asymptotic errors and likelihood profiles and develops a generalized Gibbs sampler to run a Markov chain Monte Carlo analysis that can be used to generate Bayesian posteriorsSized-Based Models implements a fully functional size-based stock assessment model using abalone as an exampleThis book continues to cover a broad range of topics related to quantitative methods and modelling. It offers a solid foundation in the skills required for the quantitative study of marine populations. Explaining important and relatively complex ideas and methods in a clear manner, the author presents full, step-by-step derivations of equations as much as possible to enable a thorough understanding of the models and methods.

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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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Regression Modeling: Methods, Theory, and Computation with SAS Review

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(More customer reviews)As a doctoral student in public health, I am always looking for more texts to add to my professional library in statistics. This book not only covers some of the basic regression methods, but also many of the much more advanced methods that I have in classes. I really like how this text explains simply the ideas behind the different methods and when to use, as well as the SAS code and the explanation of the SAS code and output. The only downside is that I think the index could be a little longer - sometimes it is difficult to find a particular model though it actually is in the text.

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Regression Modeling: Methods, Theory, and Computation with SAS provides an introduction to a diverse assortment of regression techniques using SAS to solve a wide variety of regression problems. The author fully documents the SAS programs and thoroughly explains the output produced by the programs.The text presents the popular ordinary least squares (OLS) approach before introducing many alternative regression methods. It covers nonparametric regression, logistic regression (including Poisson regression), Bayesian regression, robust regression, fuzzy regression, random coefficients regression, L1 and q-quantile regression, regression in a spatial domain, ridge regression, semiparametric regression, nonlinear least squares, and time-series regression issues. For most of the regression methods, the author includes SAS procedure code, enabling readers to promptly perform their own regression runs. A Comprehensive, Accessible Source on Regression Methodology and ModelingRequiring only basic knowledge of statistics and calculus, this book discusses how to use regression analysis for decision making and problem solving. It shows readers the power and diversity of regression techniques without overwhelming them with calculations.

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Missing Data in Longitudinal Studies: Strategies for Bayesian Modeling and Sensitivity Analysis (Chapman & Hall/CRC Monographs on Statistics & Applied Probability) Review

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(More customer reviews)Issues of missing data in longitudinal studies are very important in the design and analysis of clinical trials. This is such an important statistical topic, that many excellent books have been written about it. One of the earliest and a landmark text was the book by Rubin and Little which was recently updated in the second edition. Mixed linear models for longitudinal data provide an effective method for dealing with several types of missingness as does multiple imputation. Pattern mixture models are also very useful. Molenberghs and Kennard, Verbeke and Molenberghs and Rubin all cover these topic well in their excellent texts.
What then is the advantage of this text by Daniels and Hogan?
1. It is slightly more current than the others
2. It combines theory and application very nicely
3. A series of seven real data sets from real clinical trials and epidemiologic studies are presented up front in Chapter 1 and used throughout to illustrate practical advantages and disadvantages of the various techniques covered in the latter chapters
4. It covers Bayesian modeling and sensitivity analysis in more depth that most of its competitors
Only Molenberghs and Kennard match it in the depth of coverage on theory and applications. But they do not provide the coverage of Bayesian methods the way Daniels and Hogan do.
For these reasons I recommend this book to the practicing biostatisticians working on clinical trials even if the texts listed below are alresdy on their bookshelves.
I) Diggle, P. J., Heagerty, P., Liang, K.-Y. and Zeger, S. L. (2002). "Analysis of Longitudinal Data" 2nd Edition. Oxfrod University Press, Oxford.
II) Fitzmaurice, G. M., Laird, N.M. and Ware, J. H. (2004). "Applied ongitudinal Analysis". John Wiley & Sons, New York.
III) Little, R. J. A. and Rubin, D. B. (2002) "Statistical Analysis with Missing Data" 2nd Edition, John Wiley & Sons, New York
IV) Molenberghs, G and Kennard, M. G. (2007). "Missing Data in Clinical Studies" John Wiley & Sons, Chichester.
V) Molenberghs, G. and Verbeke, G. (2005). "Models for Discrete Longitudinal Data". Springer-Verlag, New York.
VI) Pinheiro, J. C. and Bates, D. M. (2000). "Mixed Effects Models in S and S-Plus". Springer-Verlag, New York.
VII) Rubin, D. B. (1987). "Multiple Imputation for Nonresponse in Surveys" John Wiley & Sons, New York.
VIII) Tsiatis, A. A. (2006). "Semiparametric Theory and Missing Data" Dpringer-Verlag, New York.
IX) Verbeke, G and Molenberghs, G. (1997). "Linear Mixed Models in Practice: A SAS-Oriented Approach" Springer-Verlag, New York.
X) Verbeke, G and Molenberghs, G. (2000). "Linear Mixed Models for Longitudinal Data" Springer-Verlag, New York.


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Drawing from the authors' own work and from the most recent developments in the field, Missing Data in Longitudinal Studies: Strategies for Bayesian Modeling and Sensitivity Analysis describes a comprehensive Bayesian approach for drawing inference from incomplete data in longitudinal studies. To illustrate these methods, the authors employ several data sets throughout that cover a range of study designs, variable types, and missing data issues.
The book first reviews modern approaches to formulate and interpret regression models for longitudinal data. It then discusses key ideas in Bayesian inference, including specifying prior distributions, computing posterior distribution, and assessing model fit. The book carefully describes the assumptions needed to make inferences about a full-data distribution from incompletely observed data. For settings with ignorable dropout, it emphasizes the importance of covariance models for inference about the mean while for nonignorable dropout, the book studies a variety of models in detail. It concludes with three case studies that highlight important features of the Bayesian approach for handling nonignorable missingness.
With suggestions for further reading at the end of most chapters as well as many applications to the health sciences, this resource offers a unified Bayesian approach to handle missing data in longitudinal studies.

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Basics of Structural Equation Modeling Review

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(More customer reviews)I'm working on my Ph.D. using SEM. This book was very, very helpful. In fact out of about 20 books that I used, this was the most simple and easy to understand.
Buy it!

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Statistical Modeling for Biomedical Researchers: A Simple Introduction to the Analysis of Complex Data (Cambridge Medicine) Review

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(More customer reviews)I used this book as the text for a biostatistics class that used STATA as the statistitical package. I found the organization, problems, and the STATA output the book provides, all very helpful. In addition, as I moved systematically through the book, the tips regarding using the STATA features were key to my learning many of the practical aspects of the STATA program.

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For biomedical researchers, the new edition of this standard text guides readers in the selection and use of advanced statistical methods and the presentation of results to clinical colleagues. It assumes no knowledge of mathematics beyond high school level and is accessible to anyone with an introductory background in statistics. The Stata statistical software package is used to perform the analyses, in this edition employing the intuitive version 10. Topics covered include linear, logistic and Poisson regression, survival analysis, fixed-effects analysis of variance, and repeated-measure analysis of variance. Restricted cubic splines are used to model non-linear relationships. Each method is introduced in its simplest form and then extended to cover more complex situations. An appendix will help the reader select the most appropriate statistical methods for their data. The text makes extensive use of real data sets available online through Vanderbilt University.

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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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