List of Figures xvii List of Tables xxi Preface xxiii Acknowledgments xxv Part I THE PRELIMINARIES 1 WhyR? 3 1.1 Why R? 3 1.2 R Installation 5 1.3 There is Nothing such as PRACTICALS 5 1.4 Datasets in R and Internet 6 1.4.1 List of Web-sites containing DATASETS 7 1.4.2 Antique Datasets 8 1.5 http://cran.r-project.org 9 1.5.1 http://r-project.org 10 1.5.2 http://www.cran.r-project.org/web/views/ 10 1.5.3 Is subscribing to R-Mailing List useful? 10 1.6 R and its Interface with other Software 11 1.7 help and/or? 11 1.8 R Books 12 1.9 A Road Map 13 2 The R Basics 15 2.1 Introduction 15 2.2 Simple Arithmetics and a Little Beyond 16 2.2.1 Absolute Values, Remainders, etc. 16 2.2.2 round, floor, etc. 17 2.2.3 Summary Functions 18 2.2.4 Trigonometric Functions 18 2.2.5 Complex Numbers 19 2.2.6 Special Mathematical Functions 21 2.3 Some Basic R Functions 22 2.3.1 Summary Statistics 23 2.3.2 is, as, is.na, etc. 25 2.3.3 factors, levels, etc. 26 2.3.4 Control Programming 27 2.3.5 Other Useful Functions 29 2.3.6 Calculus* 31 2.4 Vectors and Matrices in R 33 2.4.1 Vectors 33 2.4.2 Matrices 36 2.5 Data Entering and Reading from Files 41 2.5.1 Data Entering 41 2.5.2 Reading Data from External Files 43 2.6 Working with Packages 44 2.7 R Session Management 45 2.8 Further Reading 46 2.9 Complements, Problems, and Programs 46 3 Data Preparation and Other Tricks 49 3.1 Introduction 49 3.2 Manipulation with Complex Format Files 50 3.3 Reading Datasets of Foreign Formats 55 3.4 Displaying R Objects 56 3.5 Manipulation Using R Functions 57 3.6 Working with Time and Date 59 3.7 Text Manipulations 62 3.8 Scripts and Text Editors for R 64 3.8.1 Text Editors for Linuxians 64 3.9 Further Reading 65 3.10 Complements, Problems, and Programs 65 4 Exploratory Data Analysis 67 4.1 Introduction: The Tukey s School of Statistics 67 4.2 Essential Summaries of EDA 68 4.3 Graphical Techniques in EDA 71 4.3.1 Boxplot 71 4.3.2 Histogram 76 4.3.3 Histogram Extensions and the Rootogram 79 4.3.4 Pareto Chart 81 4.3.5 Stem-and-Leaf Plot 84 4.3.6 Run Chart 88 4.3.7 Scatter Plot 89 4.4 Quantitative Techniques in EDA 91 4.4.1 Trimean 91 4.4.2 Letter Values 92 4.5 Exploratory Regression Models 95 4.5.1 Resistant Line 95 4.5.2 Median Polish 98 4.6 Further Reading 99 4.7 Complements, Problems, and Programs 100 Part II PROBABILITY AND INFERENCE 5 Probability Theory 105 5.1 Introduction 105 5.2 Sample Space, Set Algebra, and Elementary Probability 106 5.3 Counting Methods 113 5.3.1 Sampling: The Diverse Ways 114 5.3.2 The Binomial Coefficients and the Pascals Triangle 118 5.3.3 Some Problems Based on Combinatorics 119 5.4 Probability: A Definition 122 5.4.1 The Prerequisites 122 5.4.2 The Kolmogorov Definition 127 5.5 Conditional Probability and Independence 130 5.6 Bayes Formula 132 5.7 Random Variables, Expectations, and Moments 133 5.7.1 The Definition 133 5.7.2 Expectation of Random Variables 136 5.8 Distribution Function, Characteristic Function, and Moment Generation Function 143 5.9 Inequalities 145 5.9.1 The Markov Inequality 145 5.9.2 The Jensen s Inequality 145 5.9.3 The Chebyshev Inequality 146 5.10 Convergence of Random Variables 146 5.10.1 Convergence in Distributions 147 5.10.2 Convergence in Probability 150 5.10.3 Convergence in rth Mean 150 5.10.4 Almost Sure Convergence 151 5.11 The Law of Large Numbers 152 5.11.1 The Weak Law of Large Numbers 152 5.12 The Central Limit Theorem 153 5.12.1 The de Moivre-Laplace Central Limit Theorem 153 5.12.2 CLT for iid Case 154 5.12.3 The Lindeberg-Feller CLT 157 5.12.4 The Liapounov CLT 162 5.13 Further Reading 165 5.13.1 Intuitive, Elementary, and First Course Source 165 5.13.2 The Classics and Second Course Source 166 5.13.3 The Problem Books 167 5.13.4 Other Useful Sources 167 5.13.5 R for Probability 167 5.14 Complements, Problems, and Programs 167 6 Probability and Sampling Distributions 171 6.1 Introduction 171 6.2 Discrete Univariate Distributions 172 6.2.1 The Discrete Uniform Distribution 172 6.2.2 The Binomial Distribution 173 6.2.3 The Geometric Distribution 176 6.2.4 The Negative Binomial Distribution 178 6.2.5 Poisson Distribution 179 6.2.6 The Hypergeometric Distribution 182 6.3 Continuous Univariate Distributions 184 6.3.1 The Uniform Distribution 184 6.3.2 The Beta Distribution 186 6.3.3 The Exponential Distribution 187 6.3.4 The Gamma Distribution 188 6.3.5 The Normal Distribution 189 6.3.6 The Cauchy Distribution 191 6.3.7 The t-Distribution 193 6.3.8 The Chi-square Distribution 193 6.3.9 The F-Distribution 194 6.4 Multivariate Probability Distributions 194 6.4.1 The Multinomial Distribution 194 6.4.2 Dirichlet Distribution 195 6.4.3 The Multivariate Normal Distribution 195 6.4.4 The Multivariate t Distribution 196 6.5 Populations and Samples 196 6.6 Sampling from the Normal Distributions 197 6.7 Some Finer Aspects of Sampling Distributions 201 6.7.1 Sampling Distribution of Median 201 6.7.2 Sampling Distribution of Mean of Standard Distributions 201 6.8 Multivariate Sampling Distributions 203 6.8.1 Noncentral Univariate Chi-square, t, and F Distributions 203 6.8.2 Wishart Distribution 205 6.8.3 Hotellings T2 Distribution 206 6.9 Bayesian Sampling Distributions 206 6.10 Further Reading 207 6.11 Complements, Problems, and Programs 208 7 Parametric Inference 209 7.1 Introduction 209 7.2 Families of Distribution 210 7.2.1 The Exponential Family 212 7.2.2 Pitman Family 213 7.3 Loss Functions 214 7.4 Data Reduction 216 7.4.1 Sufficiency 217 7.4.2 Minimal Sufficiency 219 7.5 Likelihood and Information 220 7.5.1 The Likelihood Principle 220 7.5.2 The Fisher Information 226 7.6 Point Estimation 231 7.6.1 Maximum Likelihood Estimation 231 7.6.2 Method of Moments Estimator 239 7.7 Comparison of Estimators 241 7.7.1 Unbiased Estimators 241 7.7.2 Improving Unbiased Estimators 243 7.8 Confidence Intervals 245 7.9 Testing Statistical Hypotheses The Preliminaries 246 7.10 The Neyman-Pearson Lemma 251 7.11 Uniformly Most Powerful Tests 256 7.12 Uniformly Most Powerful Unbiased Tests 260 7.12.1 Tests for the Means: One- and Two-Sample t-Test 263 7.13 Likelihood Ratio Tests 265 7.13.1 Normal Distribution: One-Sample Problems 266 7.13.2 Normal Distribution: Two-Sample Problem for the Mean 269 7.14 Behrens-Fisher Problem 270 7.15 Multiple Comparison Tests 271 7.15.1 Bonferroni s Method 272 7.15.2 Holm s Method 273 7.16 The EM Algorithm* 274 7.16.1 Introduction 274 7.16.2 The Algorithm 274 7.16.3 Introductory Applications 275 7.17 Further Reading 280 7.17.1 Early Classics 280 7.17.2 Texts from the Last 30 Years 281 7.18 Complements, Problems, and Programs 281 8 Nonparametric Inference 283 8.1 Introduction 283 8.2 Empirical Distribution Function and Its Applications 283 8.2.1 Statistical Functionals 285 8.3 The Jackknife and Bootstrap Methods 288 8.3.1 The Jackknife 288 8.3.2 The Bootstrap 289 8.3.3 Bootstrapping Simple Linear Model* 292 8.4 Non-parametric Smoothing 294 8.4.1 Histogram Smoothing 294 8.4.2 Kernel Smoothing 297 8.4.3 Nonparametric Regression Models* 300 8.5 Non-parametric Tests 304 8.5.1 The Wilcoxon Signed-Ranks Test 305 8.5.2 The Mann-Whitney test 308 8.5.3 The Siegel-Tukey Test 309 8.5.4 The Wald-Wolfowitz Run Test 311 8.5.5 The Kolmogorov-Smirnov Test 312 8.5.6 Kruskal-Wallis Test* 314 8.6 Further Reading 315 8.7 Complements, Problems, and Programs 316 9 Bayesian Inference 317 9.1 Introduction 317 9.2 Bayesian Probabilities 317 9.3 The Bayesian Paradigm for Statistical Inference 321 9.3.1 Bayesian Sufficiency and the Principle 321 9.3.2 Bayesian Analysis and Likelihood Principle 322 9.3.3 Informative and Conjugate Prior 322 9.3.4 Non-informative Prior 323 9.4 Bayesian Estimation 323 9.4.1 Inference for Binomial Distribution 323 9.4.2 Inference for the Poisson Distribution 326 9.4.3 Inference for Uniform Distribution 327 9.4.4 Inference for Exponential Distribution 328 9.4.5 Inference for Normal Distributions 329 9.5 The Credible Intervals 332 9.6 Bayes Factors for Testing Problems 333 9.7 Further Reading 334 9.8 Complements, Problems, and Programs 335 Part III STOCHASTIC PROCESSES AND MONTE CARLO 10 Stochastic Processes 339 10.1 Introduction 339 10.2 Kolmogorov s Consistency Theorem 340 10.3 Markov Chains 341 10.3.1 The m-Step TPM 344 10.3.2 Classification of States 345 10.3.3 Canonical Decomposition of an Absorbing Markov Chain 347 10.3.4 Stationary Distribution and Mean First Passage Time of an Ergodic Markov Chain 350 10.3.5 Time Reversible Markov Chain 352 10.4 Application of Markov Chains in Computational Statistics 352 10.4.1 The Metropolis-Hastings Algorithm 353 10.4.2 Gibbs Sampler 354 10.4.3 Illustrative Examples 355 10.5 Further Reading 361 10.6 Complements, Problems, and Programs 361 11 Monte Carlo Computations 363 11.1 Introduction 363 11.2 Generating the (Pseudo-) Random Numbers 364 11.2.1 Useful Random Generators 364 11.2.2 Probability Through Simulation 366 11.3 Simulation from Probability Distributions and Some Limit Theorems 373 11.3.1 Simulation from Discrete Distributions 373 11.3.2 Simulation from Continuous Distributions 380 11.3.3 Understanding Limit Theorems through Simulation 383 11.3.4 Understanding The Central Limit Theorem 386 11.4 Monte Carlo Integration 388 11.5 The Accept-Reject Technique 390 11.6 Application to Bayesian Inference 394 11.7 Further Reading 397 11.8 Complements, Problems, and Programs 397 Part IV LINEAR MODELS 12 Linear Regression Models 401 12.1 Introduction 401 12.2 Simple Linear Regression Model 402 12.2.1 Fitting a Linear Model 403 12.2.2 Confidence Intervals 405 12.2.3 The Analysis of Variance (ANOVA) 407 12.2.4 The Coefficient of Determination 409 12.2.5 The lm Function from R 410 12.2.6 Residuals for Validation of the Model Assumptions 412 12.2.7 Prediction for the Simple Regression Model 416 12.2.8 Regression through the Origin 417 12.3 The Anscombe Warnings and Regression Abuse 418 12.4 Multiple Linear Regression Model 421 12.4.1 Scatter Plots: A First Look 422 12.4.2 Other Useful Graphical Methods 423 12.4.3 Fitting a Multiple Linear Regression Model 427 12.4.4 Testing Hypotheses and Confidence Intervals 429 12.5 Model Diagnostics for the Multiple Regression Model 433 12.5.1 Residuals 433 12.5.2 Influence and Leverage Diagnostics 436 12.6 Multicollinearity 441 12.6.1 Variance Inflation Factor 442 12.6.2 Eigen System Analysis 443 12.7 Data Transformations 445 12.7.1 Linearization 445 12.7.2 Variance Stabilization 447 12.7.3 Power Transformation 449 12.8 Model Selection 451 12.8.1 Backward Elimination 453 12.8.2 Forward and Stepwise Selection 456 12.9 Further Reading 458 12.9.1 Early Classics 458 12.9.2 Industrial Applications 458 12.9.3 Regression Details 458 12.9.4 Modern Regression Texts 458 12.9.5 R for Regression 458 12.10 Complements, Problems, and Programs 458 13 Experimental Designs 461 13.1 Introduction 461 13.2 Principles of Experimental Design 461 13.3 Completely Randomized Designs 462 13.3.1 The CRD Model 462 13.3.2 Randomization in CRD 463 13.3.3 Inference for the CRD Models 465 13.3.4 Validation of Model Assumptions 470 13.3.5 Contrasts and Multiple Testing for the CRD Model 472 13.4 Block Designs 477 13.4.1 Randomization and Analysis of Balanced Block Designs 477 13.4.2 Incomplete Block Designs 481 13.4.3 Latin Square Design 484 13.4.4 Graeco Latin Square Design 487 13.5 Factorial Designs 490 13.5.1 Two Factorial Experiment 491 13.5.2 Three-Factorial Experiment 496 13.5.3 Blocking in Factorial Experiments 502 13.6 Further Reading 504 13.7 Complements, Problems, and Programs 504 14 Multivariate Statistical Analysis - I 507 14.1 Introduction 507 14.2 Graphical Plots for Multivariate Data 507 14.3 Definitions, Notations, and Summary Statistics for Multivariate Data 511 14.3.1 Definitions and Data Visualization 511 14.3.2 Early Outlier Detection 517 14.4 Testing for Mean Vectors : One Sample 520 14.4.1 Testing for Mean Vector with Known Variance-Covariance Matrix 520 14.4.2 Testing for Mean Vectors with Unknown Variance-Covariance Matrix 521 14.5 Testing for Mean Vectors : Two-Samples 523 14.6 Multivariate Analysis of Variance 526 14.6.1 Wilks Test Statistic 526 14.6.2 Roy s Test 528 14.6.3 Pillai s Test Statistic 529 14.6.4 The Lawley-Hotelling Test Statistic 529 14.7 Testing for Variance-Covariance Matrix: One Sample 531 14.7.1 Testing for Sphericity 532 14.8 Testing for Variance-Covariance Matrix: k-Samples 533 14.9 Testing for Independence of Sub-vectors 536 14.10 Further Reading 538 14.11 Complements, Problems, and Programs 538 15 Multivariate Statistical Analysis - II 541 15.1 Introduction 541 15.2 Classification and Discriminant Analysis 541 15.2.1 Discrimination Analysis 542 15.2.2 Classification 543 15.3 Canonical Correlations 544 15.4 Principal Component Analysis Theory and Illustration 547 15.4.1 The Theory 547 15.4.2 Illustration Through a Dataset 549 15.5 Applications of Principal Component Analysis 553 15.5.1 PCA for Linear Regression 553 15.5.2 Biplots 556 15.6 Factor Analysis 560 15.6.1 The Orthogonal Factor Analysis Model 561 15.6.2 Estimation of Loadings and Communalities 562 15.7 Further Reading 568 15.7.1 The Classics and Applied Perspectives 568 15.7.2 Multivariate Analysis and Software 568 15.8 Complements, Problems, and Programs 569 16 Categorical Data Analysis 571 16.1 Introduction 571 16.2 Graphical Methods for CDA 572 16.2.1 Bar and Stacked Bar Plots 572 16.2.2 Spine Plots 575 16.2.3 Mosaic Plots 577 16.2.4 Pie Charts and Dot Charts 580 16.2.5 Four-Fold Plots 583 16.3 The Odds Ratio 586 16.4 The Simpson s Paradox 588 16.5 The Binomial, Multinomial, and Poisson Models 589 16.5.1 The Binomial Model 589 16.5.2 The Multinomial Model 590 16.5.3 The Poisson Model 591 16.6 The Problem of Overdispersion 593 16.7 The 2- Tests of Independence 593 16.8 Further Reading 595 16.9 Complements, Problems, and Programs 595 17 Generalized Linear Models 597 17.1 Introduction 597 17.2 Regression Problems in Count/Discrete Data 597 17.3 Exponential Family and the GLM 600 17.4 The Logistic Regression Model 601 17.5 Inference for the Logistic Regression Model 602 17.5.1 Estimation of the Regression Coefficients and Related Parameters 602 17.5.2 Estimation of the Variance-Covariance Matrix of 606 17.5.3 Confidence Intervals and Hypotheses Testing for the Regression Coefficients 607 17.5.4 Residuals for the Logistic Regression Model 608 17.5.5 Deviance Test and Hosmer-Lemeshow Goodness-of-Fit Test 611 17.6 Model Selection in Logistic Regression Models 613 17.7 Probit Regression 618 17.8 Poisson Regression Model 621 17.9 Further Reading 625 17.10 Complements, Problems, and Programs 626 Appendix A Open Source Software An Epilogue 627 Appendix B The Statistical Tables 631 Bibliography 633 Author Index 643 Subject Index 649 R Codes 659