## Table of contents for Statistical modelling in R / Murray Aitkin, Brian Francis, John Hinde.

Bibliographic record and links to related information available from the Library of Congress catalog.

Note: Contents data are machine generated based on pre-publication provided by the publisher. Contents may have variations from the printed book or be incomplete or contain other coding. ```Contents
1 Introducing R 1
1.1 Statistical packages and statistical modelling 1
1.2 Getting started in R 1
1.3 Reading data into R 3
1.4 Assignment and data generation 6
1.5 Displaying data 8
1.6 Data structures and the workspace 9
1.7 Transformations and data modification 11
1.8 Functions and suffixing 12
1.8.1 Structure functions 13
1.8.2 Mathematical functions 13
1.8.3 Logical operators 14
1.8.4 Control functions 14
1.8.5 Statistical functions 14
1.8.6 Random numbers 15
1.8.7 Suffixes in expressions 16
1.8.8 Extracting subsets of data 17
1.8.9 Recoding variates and factors into new factors 17
1.9 Graphical facilities 18
1.10 Text functions 21
1.11 Writing your own functions 22
1.12 Sorting and tabulation 23
1.13 Editing R code 26
1.14 Installing and using packages 27
2 Statistical modelling and inference 28
2.1 Statistical models 28
2.2 Types of variables 30
2.3 Population models 31
2.4 Random sampling 44
2.5 The likelihood function 44
2.6 Inference for single parameter models 46
2.6.1 Comparing two simple hypotheses 47
2.6.2 Information about a single parameter 49
2.6.3 Comparing a simple null hypothesis and a composite alternative 54
2.7 Inference with nuisance parameters 58
2.7.1 Profile likelihoods 59
2.7.2 Marginal likelihood for the variance 63
2.7.3 Likelihood normalizing transformations 66
2.7.4 Alternative test procedures 68
2.7.5 Bayes inference 71
2.7.6 Binomial model 74
2.7.7 Hypergeometric sampling from finite populations 80
2.8 The effect of the sample design on inference 81
2.9 The exponential family 82
2.9.1 Mean and variance 83
2.9.2 Generalized linear models 83
2.9.3 Maximum likelihood fitting of the GLM 84
2.9.4 Model comparisons through maximized likelihoods 87
2.10 Likelihood inference without models 89
2.10.1 Likelihoods for percentiles 89
2.10.2 Empirical likelihood 92
3 Regression and analysis of variance 97
3.1 An example 97
3.2 Strategies for model simplification 107
3.3 Stratified, weighted and clustered samples 111
3.4 Model criticism 114
3.4.1 Mis-specification of the probability distribution 116
3.4.2 Mis-specification of the link function 119
3.4.3 The occurrence of aberrant and influential observations 119
3.4.4 Mis-specification of the systematic part of the model 123
3.5 The Box-Cox transformation family 123
3.6 Modelling and background information 126
3.7 Link functions and transformations 136
3.8 Regression models for prediction 138
3.9 Model choice and mean square prediction error 140
3.10 Model selection through cross-validation 141
3.11 Reduction of complex regression models 144
3.12 Sensitivity of the Box-Cox transformation 153
3.13 The use of regression models for calibration 156
3.14 Measurement error in the explanatory variables 159
3.15 Factorial designs 161
3.16 Unbalanced cross-classifications 168
3.16.1 The Bennett hostility data 168
3.16.2 ANOVA of the cross-classification 170
3.16.3 Regression analysis of the cross-classification 174
3.16.4 Statistical package treatments of cross-classifications 176
3.17 Missing data 178
3.18 Approximate methods for missing data 180
3.19 Modelling of variance heterogeneity 180
3.19.1 Poison example 184
3.19.2 Tree example 191
4 Binary response data 195
4.1 Binary responses 195
4.2 Transformations and link functions 197
4.2.1 Profile likelihoods for functions of parameters 202
4.3 Model criticism 207
4.3.1 Mis-specification of the probability distribution 207
4.3.2 Mis-specification of the link function 207
4.3.3 The occurrence of aberrant and influential observations. 207
4.4 Binary data with continuous covariates 208
4.5 Contingency table construction from binary data 223
4.6 The prediction of binary outcomes 235
4.7 Profile and conditional likelihoods in 2 2 tables 242
4.8 Three-dimensional contingency tables with a binary response 246
4.8.1 Prenatal care and infant mortality 246
4.8.2 Coronary heart disease 248
4.9 Multidimensional contingency tables with a binary response 255
5 Multinomial and Poisson response data 269
5.1 The Poisson distribution 269
5.2 Cross-classified counts 271
5.3 Multicategory responses 279
5.4 Multinomial logit model 285
5.5 The Poisson-multinomial relation 287
5.6 Fitting the multinomial logit model 293
5.7 Ordered response categories 298
5.7.1 Common slopes for the regressions 299
5.7.2 Linear trend over response categories 301
5.7.3 Proportional slopes 304
5.7.4 The continuation ratio model 304
5.7.5 Other models 308
5.8 An Example 310
5.8.1 Multinomial logit model 313
5.8.2 Continuation ratio model 320
5.9 Structured multinomial responses 330
5.9.1 Independent outcomes 331
5.9.2 Correlated outcomes 339
6 Survival data 347
6.1 Introduction 347
6.2 The exponential distribution 347
6.3 Fitting the exponential distribution 349
6.4 Model criticism 354
6.5 Comparison with the normal family 361
6.6 Censoring 364
6.7 Likelihood function for censored observations 365
6.8 Probability plotting with censored data: the Kaplan-Meier estimator 368
6.9 The gamma distribution 377
6.9.1 Maximum likelihood with uncensored data 379
6.9.2 Maximum likelihood with censored data 382
6.9.3 Double modelling 384
6.10 The Weibull distribution 388
6.11 Maximum likelihood fitting of the Weibull distribution 390
6.12 The extreme value distribution 394
6.13 The reversed extreme value distribution 397
6.14 Survivor function plotting for the Weibull and extreme value distributions 398
6.15 The Cox proportional hazards model and the piecewise exponential distribution 400
6.16 Maximum likelihood fitting of the piecewise exponential distribution 403
6.17 Examples 404
6.18 The logistic and log-logistic distributions 407
6.19 The normal and lognormal distributions 411
6.20 Evaluating the proportional hazard assumption 414
6.21 Competing risks 420
6.22 Time-dependent explanatory variables 427
6.23 Discrete time models 427
7 Finite mixture models 433
7.1 Introduction 433
7.2 Example - girl birthweights 434
7.3 Finite mixtures of distributions 434
7.4 Maximum likelihood in finite mixtures 435
7.5 Standard errors 437
7.6 Testing for the number of components 440
7.6.1 Example 443
7.7 Likelihood 'spikes' 448
7.8 Galaxy data 450
7.9 Kernel density estimates 458
8 Random effect models 461
8.1 Overdispersion 461
8.1.1 Testing for overdispersion 464
8.2 Conjugate random effects 466
8.2.1 Normal kernel: the t-distribution 466
8.2.2 Poisson kernel: the negative binomial distribution 472
8.2.3 Binomial kernel: beta-binomial distribution 477
8.2.4 Gamma kernel 478
8.2.5 Difficulties with the conjugate approach 478
8.3 Normal random effects 479
8.3.1 Predicting from the normal random effect model 481
8.4 Gaussian quadrature examples 481
8.4.1 Overdispersion model fitting 481
8.4.2 Poisson - the fabric fault data 482
8.4.3 Binomial - the toxoplasmosis data 484
8.5 Other specified random effect distributions 487
8.6 Arbitrary random effects 487
8.7 Examples 489
8.7.1 The fabric fault data 489
8.7.2 The toxoplasmosis data 492
8.7.3 Leukaemia remission data 493
8.7.4 The Brownlee stack-loss data 493
8.8 Random coefficient regression models 496
8.8.1 Example - the fabric fault data 498
8.9 Algorithms for mixture fitting 499
8.9.1 The trypanosome data 499
8.10 Modelling the mixing probabilities 503
8.11 Mixtures of mixtures 504
9 Variance component models 508
9.1 Models with shared random effects 508
9.2 The normal/normal model 508
9.3 Exponential family two-level models 511
9.4 Other approaches 513
9.5 NPML estimation of the masses and mass-points 514
9.6 Random coefficient models 514
9.7 Variance component model fitting 515
9.7.1 Children's height development 516
9.7.2 Multi-centre trial of beta-blockers 524
9.7.3 Longitudinal study of obesity 530
9.8 Autoregressive random effect models 537
9.9 Latent variable models 543
9.9.1 The normal factor model 543
9.10 IRT models 544
9.10.1 The Rasch model 544
9.10.2 The two-parameter model 545
9.10.3 The three-parameter logit (3PL) model 547
9.10.4 Example - The Law School Aptitude Test (LSAT) 547
9.11 Spatial dependence 551
9.12 Multivariate correlated responses 552
9.13 Discreteness of the NPML estimate 552
Bibliography 554
R function and constant index 567
Dataset index 571
Subject index 574
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Library of Congress Subject Headings for this publication:

R (Computer program language).
Mathematical statistics -- Data processing.