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How This Book Is Organized x CONTENTS 3 Reformulating Ordinary Regression Analysis in Matrix Notation 30 3.1 Writing the Ordinary Regression Equation in Matrix Notation 31 3.1.1 Example 32 3.2 Obtaining the Least-Squares Estimator βˆ in Matrix Notation 33 3.2.1 Example: Matrices in Regression Analysis 34 3.3 List of Matrix Operations to Know 36 4 Variance Matrices and Linear Transformations 38 4.1 Variance and Correlation Matrices 38 4.1.1 Example 40 4.2 How to Obtain the Variance of a Linear Transformation 40 4.2.1 Two Variables 40 4.2.2 Many Variables 42 5 Variance Matrices of Estimators of Regression Coefficients 51 5.1 Usual Standard Error of Least-Squares Estimator of Regression Slope in Nonmatrix Formulation 51 5.2 Standard Errors of Least-Squares Regression Estimators in Matrix Notation 52 5.2.1 Example 53 5.3 The Large Sample Variance Matrix of Maximum Likelihood Estimators 54 5.4 Tests and Confidence Intervals 56 5.4.1 Example-Comparing PROC REG and PROC MIXED 57 6 Dealing with Unequal Variance Around the Regression Line 62 6.1 Ordinary Least Squares with Unequal Variance 62 6.1.1 Examples 64 6.2 Analysis Taking Unequal Variance into Account 66 6.2.1 The Functional Transformation Approach 66 6.2.2 The Linear Transformation Approach 68 6.2.3 Standard Errors of Weighted Regression Estimators 73 Output Packet III: Applying the Empirical Option to Adjust Standard Errors 75 Output Packet IV: Analyses with Transformation of the Outcome Variable to Equalize Residual Variance 83 Output Packet V: Weighted Regression Analyses of GHb Data on Age 93 CONTENTS xi 7 Application of Weighting with Probability Sampling and Nonresponse 97 7.1 Sample Surveys with Unequal Probability Sampling 98 7.1.1 Example 101 7.2 Examining the Impact of Nonresponse 102 7.2.1 Example (of Reweighting as Well as Some SAS Manipulations) 104 7.2.2 A Few Comments on Weighting by a Variable Versus Including it in the Regression Model 107 Output Packet VI: Survey and Missing Data Weights 109 8 Principles in Dealing with Correlated Data 119 8.1 Analysis of Correlated Data by Ordinary Unweighted Least-Squares Estimation 120 8.1.1 Example 121 8.1.2 Deriving the Variance Estimator 122 8.1.3 Example 124 8.2 Specifying Correlation and Variance Matrices 124 8.3 The Least-Squares Equation Incorporating Correlation 126 8.3.1 Another Application of the Spectral Theorem 127 8.4 Applying the Spectral Theorem to the Regression Analysis of Correlated Data 128 8.5 Analysis of Correlated Data by Maximum Likelihood 129 8.5.1 Non equal Variance 130 8.5.2 Correlated Errors 131 8.5.3 Example 132 Output Packet VII: Analysis of Longitudinal Data in Wisconsin Sleep Cohort 135 9 A Further Study of How the Transformation Works with Correlated Data 145 9.1 Why Would βW and βB Differ? 147 9.2 How the Between- and Within-Individual Estimators are Combined 149 9.3 How to Proceed in Practice 151 9.3.1 Example 152 Output Packet VIII: Investigating and Fitting Within- and Between-Individual Effects 154 10 Random Effects 156 10.1 Random Intercept 156 10.1.1 Example 159 xii CONTENTS 10.1.2 Example 161 10.2 Random Slopes 161 10.2.1 Example 165 10.3 Obtaining “The Best” Estimates of Individual Intercepts and Slopes 167 10.3.1 Example 167 Output Packet IX: Fitting Random Effects Models 169 11 The Normal Distribution and Likelihood Revisited 181 11.1 PROC GENMOD 182 11.1.1 Example 183 Output Packet X: Introducing PROC GENMOD 184 12 The Generalization to Non-normal Distributions 190 12.1 The Exponential Family 190 12.1.1 The Binomial Distribution 192 12.1.2 The Poisson Distribution 193 12.1.3 Example 194 12.2 Score Equations for the Exponential Family and the Canonical Link 194 12.3 Other Link Functions 196 12.3.1 Example 197 13 Modeling Binomial and Binary Outcomes 199 13.1 A Brief Review of Logistic Regression 199 13.1.1 Example: Review of the Output from PROC LOGIST 200 13.2 Analysis of Binomial Data in the Generalized Linear Models Framework 202 13.2.1 Example of Logistic Regression with Binary Outcome 206 13.2.2 Example with Binomial Outcome 207 13.2.3 Some More Examples of Goodness-of-Fit Tests 209 13.3 Other Links for Binary and Binomial Data 209 13.3.1 Example 211 Output Packet XI: Logistic Regression Analysis with PROC LOGIST and PROC GENMOD 212 Output Packet XII: Analysis of Grouped Binomial Data 221 Output Packet XIII: Some Goodness-of-Fit Tests for Binomial Outcome 223 Output Packet XIV: Three Link Functions for Binary Outcome 229 Output Packet XV: Poisson Regression 247 Output Packet XVI: Dealing with Overdispersion in Rates 254 CONTENTS xiii 14 Modeling Poisson Outcomes—The Analysis of Rates 236 14.1 Review of Rates 236 14.1.1 Relationship Between Rate and Risk 238 14.2 Regression Analysis 239 14.3 Example with Cancer Mortality Rates 241 14.3.1 Example with Hospitalization of Infants 242 14.4 Overdispersion 243 14.4.1 Fitting a Dispersion Parameter 244 14.4.2 Fitting a Different Distribution 245 14.4.3 Using Robust Standard Errors 245 14.4.4 Applying Adjustments for Over Dispersion to the Examples 246 Output Packet XV: Poisson Regression 247 15 Modeling Correlated Outcomes with Generalized Estimating Equations 263 15.1 A Brief Review and Reformulation of the Normal Distribution, Least Squares and Likelihood 263 15.2 Further Developments for the Exponential Family 264 15.3 How are the Generalized Estimating Equations Justified? 266 15.3.1 Analysis of Longitudinal Systolic Blood Pressure by PROC MIXED and GENMOD 267 15.3.2 Analysis of Longitudinal Hypertension Data by PROC GENMOD 269 15.3.3 Analysis of Hospitalizations Among VLBW Children Up to Age 5 271 15.4 Another Way to Deal with Correlated Binary Data 273 Output Packet XVII: Mixed Versus GENMOD for Longitudinal SBP and Hypertension Data 274 Output Packet XVIII: Longitudinal Analysis of Rates 285 Output Packet XIX: Conditional Logistic Regression of Hypertension Data 288 References 290 Appendix: Matrix Operations 295 A.1 Adding Matrices 296 A.2 Multiplying Matrices by a Number 297 A.3 Multiplying Matrices by Each Other 297 A.4 The Inverse of a Matrix 299 Index
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