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Generalized Additive Models: An Introduction with R, Second Edition 2nd edition [Kietas viršelis]

4.17/5 (42 ratings by Goodreads)
  • Formatas: Hardback, 496 pages, aukštis x plotis: 234x156 mm, weight: 900 g, 5 Tables, black and white; 106 Line drawings, black and white; 39 Halftones, black and white; 145 Illustrations, black and white
  • Serija: Chapman & Hall/CRC Texts in Statistical Science
  • Išleidimo metai: 30-May-2017
  • Leidėjas: Chapman & Hall/CRC
  • ISBN-10: 1498728332
  • ISBN-13: 9781498728331
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 496 pages, aukštis x plotis: 234x156 mm, weight: 900 g, 5 Tables, black and white; 106 Line drawings, black and white; 39 Halftones, black and white; 145 Illustrations, black and white
  • Serija: Chapman & Hall/CRC Texts in Statistical Science
  • Išleidimo metai: 30-May-2017
  • Leidėjas: Chapman & Hall/CRC
  • ISBN-10: 1498728332
  • ISBN-13: 9781498728331
Kitos knygos pagal šią temą:
The first edition of this book has established itself as one of the leading references on generalized additive models (GAMs), and the only book on the topic to be introductory in nature with a wealth of practical examples and software implementation. It is self-contained, providing the necessary background in linear models, linear mixed models, and generalized linear models (GLMs), before presenting a balanced treatment of the theory and applications of GAMs and related models.

The author bases his approach on a framework of penalized regression splines, and while firmly focused on the practical aspects of GAMs, discussions include fairly full explanations of the theory underlying the methods. Use of R software helps explain the theory and illustrates the practical application of the methodology. Each chapter contains an extensive set of exercises, with solutions in an appendix or in the books R data package gamair, to enable use as a course text or for self-study.

Recenzijos

"A well-written book providing in-depth and comprehensive coverage of regression models from linear models through generalized linear and mixed models to generalized additive models. The book stands out by placing weight on geometric intuition and numerically efficient estimation algorithms, but most importantly by providing many worked-through application examples with details on model choice as well as accompanying R-code. Compared to the first edition, many new developments are included, from improved inference in generalized additive models to extensions such as response distributions outside the exponential family. As the book includes many advanced topics and the necessary theory but develops everything from the basics, it will be of interest to statistical researchers and practitioners alike. It will be a handy reference book for anyone using the popular mgcv R package and could also be used as an accompanying textbook for a series of regression courses for graduate or advanced undergraduate students." Sonja Greven, Professor, Department of Statistics, Ludwig-Maximilians-Universität München, Munich

"A great book got even better. Simon Woods focus on splines for fitting GAMs allows for a seamless integration with mixed effects models and gaussian processes, which enlarges the scope of GAMs considerably. This book and the R software are wonderful contributions to applied statistics and data science." Trevor Hastie, Stanford University

"The first edition of Simon Woods Generalized Additive Models appeared in 2006 to wide and well-deserved acclaim. Since then the field has progressed considerably; in particular Wood himself has made a stunning array of major advances. In his newly revised text, Wood expertly and engagingly guides the reader from background material on linear and generalized linear models all the way through the latest developments in generalized additive (mixed) models. For anyone seeking an up-to-date treatment of what smooth models can do, this new edition is indispensable." Philip Reiss, University of Haifa and New York University

"This excellent and well-written book covers a lot more than "merely" GAMs, with the first few chapters providing a pretty comprehensive guide to regression modelling in general. That is a boon for would-be GAM-users from applied fields such as ecology, who sometimes find themselves plunged into the deep end of statistical modelling (GAMs) without much practice in the shallow end. The presentation in this second edition now puts mixed-effect models up-front alongside generalized linear models, presenting GAMs as the glorious fruit of their union, with smooth terms being random effects. This leads to a coherent and extensible modelling framework throughout, which I would describe as broadly Bayesian but not dogmatically so. There is a quiet but consistent emphasis on sound theoretical underpinnings and computational reliability valuable in the field of smoothing, where ad hoc approaches have been rife, and where inferential principles need to be stretched hard to handle the types of model that can nowadays be fitted. The extensive examples using the mgcv R package are realistic and not over-simplified, and nicely show when enough work is enough. The theory chapters pack enough in to let an advanced user extend the machinery to broader classes of data (from my own experience); and they contain substantial new material, reflecting 10 more years of practical experience and application-driven development, for example to cope with huge datasets. The tools and the theory covered by this book and its predecessor have certainly been a major influence on my own statistical practice over the last 20 years, and I have no doubt they will continue to be." Dr. Mark Bravington, Senior research statistician, CSIRO, Australia

"The new edition substantially differs in many respects from the original edition. There are about 80 more pages adding new important results, which have been derived in the last decade. The central change is that linear mixed models theory is now already discussed very early within the second chapter. This is a clever didactical change because it makes the equivalence of smooth regression and random effect models much clearer. There are now sections on adaptive smoothing, SCOP-splines, or soap film smoothers. There is lots of modified and new material in the last section of the book on GAMs in practice: mgcv. Here you can find the analysis of several new data problems and also a section on functional data analysis. Overall the content of the second edition is now presented such that effective teaching and learning is strongly promoted. For practitioners working with the R library mgcv, this second edition describes at length all the actual issues and possibilities of this powerful set of functions. This book is definitely covering the state-of-the-art in modern smooth modelling. I strongly recommend this new edition due to all the reasons I have mentioned above." Herwig Friedl, Graz University of Technology, Austria

"This book is so much more than it says in the title! In addition to being my go-to text for generalized additive models, it provides a very clear and concise introduction to linear models, linear mixed models, generalized linear models and generalized additive mixed models. This is supplemented by accessible appendices laying out key results in maximum likelihood theory and the matrix algebra required for the theory covered in the book. The first edition of this excellent text is one of the books I consult most frequently, both for teaching and research purposes.This second edition substantially updates and expands the scope and the depth of the book. There is a new chapter on mixed effects models that expands on material in the first edition, more on GLMMs, an extended chapter on Smoothers that includes treatment of Gaussian Markov Random fields, and well-organised solutions to exercises. If you teach courses on linear models, GLMs, GLMMs, GAMs or GAMMs you will find this book a valuable resource for theoretical material, for illustrative applications, for exercises, and as a guide to using the mgcv package in your course. If you do research that may require any of the above methods, you will find that this book provides an invaluable synthesis of the areas, as well as a reference source for the technical detail of the methods. I know of very few statistics books that combine such an accessible synthesis of a broad area of statistics with the rigor and detail that allows the reader to understand the intricacies of virtually any aspect of the area. Prof Wood has a rare ability to see both the wood and the trees with incisive clarity." Prof. David Borchers, University of St Andrews

"The first edition of this book has been one of the most valuable resources both to get familiar with generalized additive models and their application, but also to get to know more about the underlying theory. In the ten years since the publication of the first edition, not only the mgcv package, but also the underlying theory have made much progress and it is therefore good to see the second edition reflecting both developments and comprising a lot of new and fascinating material. This applies in particular to many novel elements on inference in generalized additive models, e.g. a much extended overview on methods to select the smoothing parameters, but also high level inference via hypothesis testing, p-values or an Akaike information criterion that takes smoothing parameter uncertainty into account. These inferential developments are backed up by additional details on a large number of smooth terms and response distributions that significantly enhance the applicability of (extended) generalized additive models. Clearly, Simon Wood is one of the driving forces of the success of generalized additive models both due to the software he provides and due to his in-depth theoretical investigation of the underlying properties. I am wholeheartedly convinced that this book will find a wide readership and will accompany many researchers and applied scientists when either tipping their toe or diving deeply into the ocean of generalized additive models." Thomas Kneib, Georg-August-Universität Göttingen

"With this second edition, it may be safe to say that Simon Wood has made Generalized Additive Models (and its extensions) more accessible to researchers, practitioners, teachers, and students than ever before. One of my very first thoughts when looking at this book was just how lucky students are these days to have books like this one that carefully and intelligibly place such vast, powerful, and flexible modeling tools at their fingertips. His first edition had already "hit the nail on the head," but it is clear that this refined iteration was well-thought out and deliberately executed with sensitivity toward the reader. Like his code, Simon writes his textbook in an uncompromising, sensible, and approachable way. The books title is a complete understatement. For one, the first few chapters present a carefully chosen coverage of the (generalized) linear model and modern approaches to (generalized) random effect variants, which truth be told is already enough for a very nice stand-alone course. Yet he goes for far more. From the start, the reader finds balance of theory, inference, and application, all while the author earns the readers confidence through relevant and important examples using R. In fact, there is an implicit accountability of utility throughout. Case in point: an entire chapter is devoted to "GAMs in Practice." It is such a pleasure to see Simons broader approach toward extensions, e.g.: Spatial Smoothing, GAMLSS, functional regression, single-index models, Bayesian perspectives, and more. Just for added value, the appendices provide unique tool boxes, and there are also exercises to bridge teaching efforts." Professor Brian D. Marx, Louisiana State University

Praise for the first edition:

A strength of this book is the presentation style . The step-by-step instructions are complemented with clear examples and sample code . In addition to emphasizing the practical aspects of the methods, a healthy dose of theory helps the reader understand the fundamentals of the underlying approach. The generous use of graphs and plots helps visualization and enhances understanding. this is an excellent reference book for a broad audience Christine M. Anderson-Cook (Los Alamos National Laboratory), in Journal of the American Statistical Association, June 2007

"This is an amazing book. The title is an understatement. Certainly the book covers an introduction to generalized additive models (GAMs), but to get there, it is almost as if Simon has left no stone unturned. In chapter 1 the usual 'bread and butter' linear models is presented boldly. Chapter 2 continues with an accessible presentation of the generalized linear model that can be used on its own for a separate introductory course. The reader gains confidence, as if anything is possible, and the examples using software puts modern and sophisticated modeling at their fingertips. I was delighted to see the presentation of GAMs uses penalized splines - the author sorts through the clutter and presents a well-chosen toolbox. Chapter 6 brings the smoothing/GAM presentation into contemporary and state-of-the-art light, for one by making the reader aware of relationships among P-splines, mixed models, and Bayesian approaches. The author is careful and clever so that anyone at any level will have new insights from his presentation. This book modernizes and complements Hastie and Tibshirani's landmark book on the topic." Professor Brian D. Marx, Louisiana State University, USA

This attractively written advanced level text shows its style by starting with the question How old is the universe?. It serves also as a manual for the authors mgcv package, which is one of the Rs recommended packages. The style and emphasis, and the attention to practical data analysis issue, make this a highly appealing volume. I strongly recommend this book. John Maindonald, Australian National University, in Journal of Statistical Software, Vol. 16, July 2006

"In summary, the book is highly accessible and a fascinating read. It meets the authors aim of providing a fairly full, but concise, theoretical treatment, explaining how the models and methods work. I would recommend it to anyone interested in statistical modelling." Weiqi Luo, University of Leeds, in Journal of Applied Statistics, July 2007, Vol. 34, No. 5

"The book has a very wide scope. It presents theory and many examples, complete with R code. A companion package, gamair, contains all of the data and scripts, grouped by chapter. A crucial aspect of smoothing, which gets much attention, is finding good values for penalty parameters. Compared to the first edition, the size of the book has grown by around 20%. The exercises, with solutions, are still there. ...I can really recommend this book. It does not replace the R help file of the package, which is some 300 pages long. Many further practical details are explained there." -Paul Eilers (NL), ISCB June 2018 "A well-written book providing in-depth and comprehensive coverage of regression models from linear models through generalized linear and mixed models to generalized additive models. The book stands out by placing weight on geometric intuition and numerically efficient estimation algorithms, but most importantly by providing many worked-through application examples with details on model choice as well as accompanying R-code. Compared to the first edition, many new developments are included, from improved inference in generalized additive models to extensions such as response distributions outside the exponential family. As the book includes many advanced topics and the necessary theory but develops everything from the basics, it will be of interest to statistical researchers and practitioners alike. It will be a handy reference book for anyone using the popular mgcv R package and could also be used as an accompanying textbook for a series of regression courses for graduate or advanced undergraduate students." Sonja Greven, Professor, Department of Statistics, Ludwig-Maximilians-Universität München, Munich

"A great book got even better. Simon Woods focus on splines for fitting GAMs allows for a seamless integration with mixed effects models and gaussian processes, which enlarges the scope of GAMs considerably. This book and the R software are wonderful contributions to applied statistics and data science." Trevor Hastie, Stanford University

"The first edition of Simon Woods Generalized Additive Models appeared in 2006 to wide and well-deserved acclaim. Since then the field has progressed considerably; in particular Wood himself has made a stunning array of major advances. In his newly revised text, Wood expertly and engagingly guides the reader from background material on linear and generalized linear models all the way through the latest developments in generalized additive (mixed) models. For anyone seeking an up-to-date treatment of what smooth models can do, this new edition is indispensable." Philip Reiss, University of Haifa and New York University

"This excellent and well-written book covers a lot more than "merely" GAMs, with the first few chapters providing a pretty comprehensive guide to regression modelling in general. That is a boon for would-be GAM-users from applied fields such as ecology, who sometimes find themselves plunged into the deep end of statistical modelling (GAMs) without much practice in the shallow end. The presentation in this second edition now puts mixed-effect models up-front alongside generalized linear models, presenting GAMs as the glorious fruit of their union, with smooth terms being random effects. This leads to a coherent and extensible modelling framework throughout, which I would describe as broadly Bayesian but not dogmatically so. There is a quiet but consistent emphasis on sound theoretical underpinnings and computational reliability valuable in the field of smoothing, where ad hoc approaches have been rife, and where inferential principles need to be stretched hard to handle the types of model that can nowadays be fitted. The extensive examples using the mgcv R package are realistic and not over-simplified, and nicely show when enough work is enough. The theory chapters pack enough in to let an advanced user extend the machinery to broader classes of data (from my own experience); and they contain substantial new material, reflecting 10 more years of practical experience and application-driven development, for example to cope with huge datasets. The tools and the theory covered by this book and its predecessor have certainly been a major influence on my own statistical practice over the last 20 years, and I have no doubt they will continue to be." Dr. Mark Bravington, Senior research statistician, CSIRO, Australia

"The new edition substantially differs in many respects from the original edition. There are about 80 more pages adding new important results, which have been derived in the last decade. The central change is that linear mixed models theory is now already discussed very early within the second chapter. This is a clever didactical change because it makes the equivalence of smooth regression and random effect models much clearer. There are now sections on adaptive smoothing, SCOP-splines, or soap film smoothers. There is lots of modified and new material in the last section of the book on GAMs in practice: mgcv. Here you can find the analysis of several new data problems and also a section on functional data analysis. Overall the content of the second edition is now presented such that effective teaching and learning is strongly promoted. For practitioners working with the R library mgcv, this second edition describes at length all the actual issues and possibilities of this powerful set of functions. This book is definitely covering the state-of-the-art in modern smooth modelling. I strongly recommend this new edition due to all the reasons I have mentioned above." Herwig Friedl, Graz University of Technology, Austria

"This book is so much more than it says in the title! In addition to being my go-to text for generalized additive models, it provides a very clear and concise introduction to linear models, linear mixed models, generalized linear models and generalized additive mixed models. This is supplemented by accessible appendices laying out key results in maximum likelihood theory and the matrix algebra required for the theory covered in the book. The first edition of this excellent text is one of the books I consult most frequently, both for teaching and research purposes.This second edition substantially updates and expands the scope and the depth of the book. There is a new chapter on mixed effects models that expands on material in the first edition, more on GLMMs, an extended chapter on Smoothers that includes treatment of Gaussian Markov Random fields, and well-organised solutions to exercises. If you teach courses on linear models, GLMs, GLMMs, GAMs or GAMMs you will find this book a valuable resource for theoretical material, for illustrative applications, for exercises, and as a guide to using the mgcv package in your course. If you do research that may require any of the above methods, you will find that this book provides an invaluable synthesis of the areas, as well as a reference source for the technical detail of the methods. I know of very few statistics books that combine such an accessible synthesis of a broad area of statistics with the rigor and detail that allows the reader to understand the intricacies of virtually any aspect of the area. Prof Wood has a rare ability to see both the wood and the trees with incisive clarity." Prof. David Borchers, University of St Andrews

"The first edition of this book has been one of the most valuable resources both to get familiar with generalized additive models and their application, but also to get to know more about the underlying theory. In the ten years since the publication of the first edition, not only the mgcv package, but also the underlying theory have made much progress and it is therefore good to see the second edition reflecting both developments and comprising a lot of new and fascinating material. This applies in particular to many novel elements on inference in generalized additive models, e.g. a much extended overview on methods to select the smoothing parameters, but also high level inference via hypothesis testing, p-values or an Akaike information criterion that takes smoothing parameter uncertainty into account. These inferential developments are backed up by additional details on a large number of smooth terms and response distributions that significantly enhance the applicability of (extended) generalized additive models. Clearly, Simon Wood is one of the driving forces of the success of generalized additive models both due to the software he provides and due to his in-depth theoretical investigation of the underlying properties. I am wholeheartedly convinced that this book will find a wide readership and will accompany many researchers and applied scientists when either tipping their toe or diving deeply into the ocean of generalized additive models." Thomas Kneib, Georg-August-Universität Göttingen

"With this second edition, it may be safe to say that Simon Wood has made Generalized Additive Models (and its extensions) more accessible to researchers, practitioners, teachers, and students than ever before. One of my very first thoughts when looking at this book was just how lucky students are these days to have books like this one that carefully and intelligibly place such vast, powerful, and flexible modeling tools at their fingertips. His first edition had already "hit the nail on the head," but it is clear that this refined iteration was well-thought out and deliberately executed with sensitivity toward the reader. Like his code, Simon writes his textbook in an uncompromising, sensible, and approachable way. The books title is a complete understatement. For one, the first few chapters present a carefully chosen coverage of the (generalized) linear model and modern approaches to (generalized) random effect variants, which truth be told is already enough for a very nice stand-alone course. Yet he goes for far more. From the start, the reader finds balance of theory, inference, and application, all while the author earns the readers confidence through relevant and important examples using R. In fact, there is an implicit accountability of utility throughout. Case in point: an entire chapter is devoted to "GAMs in Practice." It is such a pleasure to see Simons broader approach toward extensions, e.g.: Spatial Smoothing, GAMLSS, functional regression, single-index models, Bayesian perspectives, and more. Just for added value, the appendices provide unique tool boxes, and there are also exercises to bridge teaching efforts." Professor Brian D. Marx, Louisiana State University

Praise for the first edition:

A strength of this book is the presentation style . The step-by-step instructions are complemented with clear examples and sample code . In addition to emphasizing the practical aspects of the methods, a healthy dose of theory helps the reader understand the fundamentals of the underlying approach. The generous use of graphs and plots helps visualization and enhances understanding. this is an excellent reference book for a broad audience Christine M. Anderson-Cook (Los Alamos National Laboratory), in Journal of the American Statistical Association, June 2007

"This is an amazing book. The title is an understatement. Certainly the book covers an introduction to generalized additive models (GAMs), but to get there, it is almost as if Simon has left no stone unturned. In chapter 1 the usual 'bread and butter' linear models is presented boldly. Chapter 2 continues with an accessible presentation of the generalized linear model that can be used on its own for a separate introductory course. The reader gains confidence, as if anything is possible, and the examples using software puts modern and sophisticated modeling at their fingertips. I was delighted to see the presentation of GAMs uses penalized splines - the author sorts through the clutter and presents a well-chosen toolbox. Chapter 6 brings the smoothing/GAM presentation into contemporary and state-of-the-art light, for one by making the reader aware of relationships among P-splines, mixed models, and Bayesian approaches. The author is careful and clever so that anyone at any level will have new insights from his presentation. This book modernizes and complements Hastie and Tibshirani's landmark book on the topic." Professor Brian D. Marx, Louisiana State University, USA

This attractively written advanced level text shows its style by starting with the question How old is the universe?. It serves also as a manual for the authors mgcv package, which is one of the Rs recommended packages. The style and emphasis, and the attention to practical data analysis issue, make this a highly appealing volume. I strongly recommend this book. John Maindonald, Australian National University, in Journal of Statistical Software, Vol. 16, July 2006

"In summary, the book is highly accessible and a fascinating read. It meets the authors aim of providing a fairly full, but concise, theoretical treatment, explaining how the models and methods work. I would recommend it to anyone interested in statistical modelling." Weiqi Luo, University of Leeds, in Journal of Applied Statistics, July 2007, Vol. 34, No. 5

"The book has a very wide scope. It presents theory and many examples, complete with R code. A companion package, gamair, contains all of the data and scripts, grouped by chapter. A crucial aspect of smoothing, which gets much attention, is finding good values for penalty parameters. Compared to the first edition, the size of the book has grown by around 20%. The exercises, with solutions, are still there. ...I can really recommend this book. It does not replace the R help file of the package, which is some 300 pages long. Many further practical details are explained there." -Paul Eilers (NL), ISCB June 2018

Preface xvii
1 Linear Models 1(60)
1.1 A simple linear model
2(7)
Simple least squares estimation
2(1)
1.1.1 Sampling properties of beta
3(1)
1.1.2 So how old is the universe?
4(3)
1.1.3 Adding a distributional assumption
7(4)
Testing hypotheses about beta
7(1)
Confidence intervals
8(1)
1.2 Linear models in general
9(2)
1.3 The theory of linear models
11(8)
1.3.1 Least squares estimation of beta
12(1)
1.3.2 The distribution of beta
13(1)
1.3.3 (betai-betai)/sigmabetai~tn-p
13(1)
1.3.4 F-ratio results I
14(1)
1.3.5 F-ratio results II
14(2)
1.3.6 The influence matrix
16(1)
1.3.7 The residuals, , and fitted values, mu
16(1)
1.3.8 Results in terms of X
17(1)
1.3.9 The Gauss Markov Theorem: What's special about least squares?
18(1)
1.4 The geometry of linear modelling
19(3)
1.4.1 Least squares
19(1)
1.4.2 Fitting by orthogonal decompositions
20(1)
1.4.3 Comparison of nested models
21(1)
1.5 Practical linear modelling
22(16)
1.5.1 Model fitting and model checking
23(5)
1.5.2 Model summary
28(2)
1.5.3 Model selection
30(1)
1.5.4 Another model selection example
31(4)
A follow-up
34(1)
1.5.5 Confidence intervals
35(1)
1.5.6 Prediction
36(1)
1.5.7 Co-linearity, confounding and causation
36(2)
1.6 Practical modelling with factors
38(8)
1.6.1 Identifiability
39(1)
1.6.2 Multiple factors
40(1)
1.6.3 'Interactions' of factors
41(2)
1.6.4 Using factor variables in R
43(3)
1.7 General linear model specification in R
46(1)
1.8 Further linear modelling theory
47(9)
1.8.1 Constraints I: General linear constraints
47(1)
1.8.2 Constraints II: 'Contrasts' and factor variables
48(1)
1.8.3 Likelihood
49(1)
1.8.4 Non-independent data with variable variance
50(2)
1.8.5 Simple AR correlation models
52(1)
1.8.6 AIC and Mallows' statistic
52(2)
1.8.7 The wrong model
54(1)
1.8.8 Non-linear least squares
54(2)
1.8.9 Further reading
56(1)
1.9 Exercises
56(5)
2 Linear Mixed Models 61(40)
2.1 Mixed models for balanced data
61(13)
2.1.1 A motivating example
61(4)
The wrong approach: A fixed effects linear model
62(2)
The right approach: A mixed effects model
64(1)
2.1.2 General principles
65(1)
2.1.3 A single random factor
66(3)
2.1.4 A model with two factors
69(5)
2.1.5 Discussion
74(1)
2.2 Maximum likelihood estimation
74(3)
2.2.1 Numerical likelihood maximization
76(1)
2.3 Linear mixed models in general
77(1)
2.4 Linear mixed model maximum likelihood estimation
78(8)
2.4.1 The distribution of bay, beta given theta
79(1)
2.4.2 The distribution of beta given theta
80(1)
2.4.3 The distribution of theta
81(1)
2.4.4 Maximizing the profile likelihood
81(2)
2.4.5 REML
83(1)
2.4.6 Effective degrees of freedom
83(1)
2.4.7 The EM algorithm
84(1)
2.4.8 Model selection
85(1)
2.5 Linear mixed models in R
86(9)
2.5.1 Package nlme
86(1)
2.5.2 Tree growth: An example using lme
87(4)
2.5.3 Several levels of nesting
91(2)
2.5.4 Package lme4
93(1)
2.5.5 Package mgcv
94(1)
2.6 Exercises
95(6)
3 Generalized Linear Models 101(60)
3.1 GLM theory
102(17)
3.1.1 The exponential family of distributions
103(2)
3.1.2 Fitting generalized linear models
105(2)
3.1.3 Large sample distribution of beta
107(1)
3.1.4 Comparing models
108(2)
Deviance
108(1)
Model comparison with unknown 0
109(1)
AIC
110(1)
3.1.5 Estimating phi, Pearson's statistic and Fletcher's estimator
110(1)
3.1.6 Canonical link functions
111(1)
3.1.7 Residuals
112(1)
Pearson residuals
112(1)
Deviance residuals
113(1)
3.1.8 Quasi-likelihood
113(2)
3.1.9 Tweedie and negative binomial distributions
115(1)
3.1.10 The Cox proportional hazards model for survival data
116(3)
Cumulative hazard and survival functions
118(1)
3.2 Geometry of GLMs
119(5)
3.2.1 The geometry of IRLS
121(1)
3.2.2 Geometry and IRLS convergence
122(2)
3.3 GLMs with R
124(23)
3.3.1 Binomial models and heart disease
125(6)
3.3.2 A Poisson regression epidemic model
131(5)
3.3.3 Cox proportional hazards modelling of survival data
136(2)
3.3.4 Log-linear models for categorical data
138(4)
3.3.5 Sole eggs in the Bristol channel
142(5)
3.4 Generalized linear mixed models
147(4)
3.4.1 Penalized IRLS
148(1)
3.4.2 The PQL method
149(2)
3.4.3 Distributional results
151(1)
3.5 GLMMs with R
151(5)
3.5.1 glmmPQL
151(3)
3.5.2 gam
154(1)
3.5.3 glmer
155(1)
3.6 Exercises
156(5)
4 Introducing GAMs 161(34)
4.1 Introduction
161(1)
4.2 Univariate smoothing
162(12)
4.2.1 Representing a function with basis expansions
162(4)
A very simple basis: Polynomials
162(1)
The problem with polynomials
162(2)
The piecewise linear basis
164(1)
Using the piecewise linear basis
165(1)
4.2.2 Controlling smoothness by penalizing wiggliness
166(3)
4.2.3 Choosing the smoothing parameter, lambda, by cross validation
169(3)
4.2.4 The Bayesian/mixed model alternative
172(2)
4.3 Additive models
174(6)
4.3.1 Penalized piecewise regression representation of an additive model
175(2)
4.3.2 Fitting additive models by penalized least squares
177(3)
4.4 Generalized additive models
180(2)
4.5 Summary
182(1)
4.6 Introducing package mgcv
182(9)
4.6.1 Finer control of gam
184(3)
4.6.2 Smooths of several variables
187(2)
4.6.3 Parametric model terms
189(2)
4.6.4 The mgcv help pages
191(1)
4.7 Exercises
191(4)
5 Smoothers 195(54)
5.1 Smoothing splines
195(4)
5.1.1 Natural cubic splines are smoothest interpolators
196(2)
5.1.2 Cubic smoothing splines
198(1)
5.2 Penalized regression splines
199(2)
5.3 Some one-dimensional smoothers
201(9)
5.3.1 Cubic regression splines
201(1)
5.3.2 A cyclic cubic regression spline
202(2)
5.3.3 P-splines
204(2)
5.3.4 P-splines with derivative based penalties
206(1)
5.3.5 Adaptive smoothing
207(1)
5.3.6 SCOP-splines
208(2)
5.4 Some useful smoother theory
210(4)
5.4.1 Identifiability constraints
211(1)
5.4.2 'Natural' parameterization, effective degrees of freedom and smoothing bias
211(3)
5.4.3 Null space penalties
214(1)
5.5 Isotropic smoothing
214(13)
5.5.1 Thin plate regression splines
215(6)
Thin plate splines
215(2)
Thin plate regression splines
217(1)
Properties of thin plate regression splines
218(1)
Knot-based approximation
219(2)
5.5.2 Duchon splines
221(1)
5.5.3 Splines on the sphere
222(1)
5.5.4 Soap film smoothing over finite domains
223(4)
5.6 Tensor product smooth interactions
227(10)
5.6.1 Tensor product bases
227(2)
5.6.2 Tensor product penalties
229(3)
5.6.3 ANOVA decompositions of smooths
232(2)
Numerical identifiability constraints for nested terms
233(1)
5.6.4 Tensor product smooths under shape constraints
234(1)
5.6.5 An alternative tensor product construction
235(4)
What is being penalized?
236(1)
5.7 Isotropy versus scale invariance
237(2)
5.8 Smooths, random fields and random effects
239(3)
5.8.1 Gaussian Markov random fields
240(1)
5.8.2 Gaussian process regression smoothers
241(1)
5.9 Choosing the basis dimension
242(1)
5.10 Generalized smoothing splines
243(2)
5.11 Exercises
245(4)
6 GAM theory 249(76)
6.1 Setting up the model
249(6)
6.1.1 Estimating beta given lambda
251(1)
6.1.2 Degrees of freedom and scale parameter estimation
251(1)
6.1.3 Stable least squares with negative weights
252(3)
6.2 Smoothness selection criteria
255(14)
6.2.1 Known scale parameter: UBRE
255(1)
6.2.2 Unknown scale parameter: Cross validation
256(2)
Leave-several-out cross validation
257(1)
Problems with ordinary cross validation
257(1)
6.2.3 Generalized cross validation
258(2)
6.2.4 Double cross validation
260(1)
6.2.5 Prediction error criteria for the generalized case
261(1)
6.2.6 Marginal likelihood and REML
262(2)
6.2.7 The problem with log |slambda|+
264(2)
6.2.8 Prediction error criteria versus marginal likelihood
266(2)
Unpenalized coefficient bias
267(1)
6.2.9 The 'one standard error rule' and smoother models
268(1)
6.3 Computing the smoothing parameter estimates
269(1)
6.4 The generalized Fellner-Schall method
269(3)
6.4.1 General regular likelihoods
271(1)
6.5 Direct Gaussian case and performance iteration (PQL)
272(8)
6.5.1 Newton optimization of the GCV score
273(3)
6.5.2 REML
276(4)
log |Slambda|+ and its derivatives
277(1)
The remaining derivative components
278(2)
6.5.3 Some Newton method details
280(1)
6.6 Direct nested iteration methods
280(7)
6.6.1 Prediction error criteria
282(1)
6.6.2 Example: Cox proportional hazards model
283(5)
Derivatives with respect to smoothing parameters
285(1)
Prediction and the baseline hazard
286(1)
6.7 Initial smoothing parameter guesses
287(1)
6.8 GAMM methods
288(2)
6.8.1 GAMM inference with mixed model estimation
289(1)
6.9 Bigger data methods
290(3)
6.9.1 Bigger still
291(2)
6.10 Posterior distribution and confidence intervals
293(8)
6.10.1 Nychka's coverage probability argument
294(6)
Interval limitations and simulations
296(4)
6.10.2 Whole function intervals
300(1)
6.10.3 Posterior simulation in general
300(1)
6.11 AIC and smoothing parameter uncertainty
301(3)
6.11.1 Smoothing parameter uncertainty
302(1)
6.11.2 A corrected AIC
303(1)
6.12 Hypothesis testing and p-values
304(11)
6.12.1 Approximate p-values for smooth terms
305(4)
Computing Tr
307(1)
Simulation performance
308(1)
6.12.2 Approximate p-values for random effect terms
309(3)
6.12.3 Testing a parametric term against a smooth alternative
312(1)
6.12.4 Approximate generalized likelihood ratio tests
313(2)
6.13 Other model selection approaches
315(1)
6.14 Further GAM theory
316(4)
6.14.1 The geometry of penalized regression
316(2)
6.14.2 Backfitting GAMs
318(2)
6.15 Exercises
320(5)
7 GAMs in Practice: mgcv 325(80)
7.1 Specifying smooths
325(3)
7.1.1 How smooth specification works
327(1)
7.2 Brain imaging example
328(15)
7.2.1 Preliminary modelling
329(4)
7.2.2 Would an additive structure be better?
333(1)
7.2.3 Isotropic or tensor product smooths?
334(2)
7.2.4 Detecting symmetry (with by variables)
336(1)
7.2.5 Comparing two surfaces
337(2)
7.2.6 Prediction with predict.gam
339(3)
Prediction with lpmatrix
341(1)
7.2.7 Variances of non-linear functions of the fitted model
342(1)
7.3 A smooth ANOVA model for diabetic retinopathy
343(3)
7.4 Air pollution in Chicago
346(7)
7.4.1 A single index model for pollution related deaths
349(2)
7.4.2 A distributed lag model for pollution related deaths
351(2)
7.5 Mackerel egg survey example
353(8)
7.5.1 Model development
354(3)
7.5.2 Model predictions
357(2)
7.5.3 Alternative spatial smooths and geographic regression
359(2)
7.6 Spatial smoothing of Portuguese larks data
361(4)
7.7 Generalized additive mixed models with R
365(12)
7.7.1 A space-time GAMM for sole eggs
365(6)
Soap film improvement of boundary behaviour
368(3)
7.7.2 The temperature in Cairo
371(3)
7.7.3 Fully Bayesian stochastic simulation: jagam
374(2)
7.7.4 Random wiggly curves
376(1)
7.8 Primary biliary cirrhosis survival analysis
377(6)
7.8.1 Time dependent covariates
380(3)
7.9 Location-scale modelling
383(4)
7.9.1 Extreme rainfall in Switzerland
384(3)
7.10 Fuel efficiency of cars: Multivariate additive models
387(3)
7.11 Functional data analysis
390(7)
7.11.1 Scalar on function regression
390(5)
Prostate cancer screening
391(2)
A multinomial prostate screening model
393(2)
7.11.2 Function on scalar regression: Canadian weather
395(2)
7.12 Other packages
397(1)
7.13 Exercises
398(7)
A Maximum Likelihood Estimation 405(14)
A.1 Invariance
405(1)
A.2 Properties of the expected log-likelihood
406(3)
A.3 Consistency
409(1)
A.4 Large sample distribution of theta
410(1)
A.5 The generalized likelihood ratio test (GLRT)
411(1)
A.6 Derivation of 2lambda - x2r under H0
411(3)
A.7 AIC in general
414(2)
A.8 Quasi-likelihood results
416(3)
B Some Matrix Algebra 419(10)
B.1 Basic computational efficiency
419(1)
B.2 Covariance matrices
420(1)
B.3 Differentiating a matrix inverse
420(1)
B.4 Kronecker product
421(1)
B.5 Orthogonal matrices and Householder matrices
421(1)
B.6 QR decomposition
422(1)
B.7 Cholesky decomposition
422(1)
B.8 Pivoting
423(1)
B.9 Eigen-decomposition
424(1)
B.10 Singular value decomposition
425(1)
B.11 Lanczos iteration
426(3)
C Solutions to Exercises 429(26)
C.1
Chapter 1
429(3)
C.2
Chapter 2
432(6)
C.3
Chapter 3
438(2)
C.4
Chapter 4
440(1)
C.5
Chapter 5
441(2)
C.6
Chapter 6
443(4)
C.7
Chapter 7
447(8)
Bibliography 455(12)
Index 467
Simon N. Wood is a professor of Statistical Science at the University of Bristol, UK, and author of the R package mgcv.