Preface |
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xiii | |
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1 Introduction To Bayesian Analysis For Categorical Data |
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1 | (12) |
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3 | (1) |
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1.2 Statistics as a Tool for Building Evidence |
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3 | (1) |
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4 | (2) |
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4 | (1) |
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5 | (1) |
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1.3.3 Interval and Ratio Data |
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5 | (1) |
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1.4 Obtaining and Using R Software |
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6 | (3) |
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1.5 Organization of Part I |
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9 | (4) |
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1 Probability And Inference |
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13 | (50) |
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13 | (1) |
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1.2 Samples, Populations, and Statistical Inference |
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13 | (6) |
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1.2.1 Populations versus Samples |
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13 | (2) |
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1.2.2 Representative Samples and Human Judgment |
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15 | (2) |
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1.2.3 Parameters, Statistics, and Statistical Inference |
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17 | (2) |
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19 | (15) |
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1.3.1 Addressable Questions, Sample Spaces, and Events |
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20 | (5) |
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1.3.2 Kolmogorov Axioms of Probability |
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25 | (2) |
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27 | (2) |
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1.3.4 Properties of Continuous Probability Distributions |
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29 | (5) |
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1.4 Assigning Probability Values |
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34 | (11) |
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1.4.1 Problems with Equal-Probability Assignment |
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34 | (1) |
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1.4.2 Relative-Frequency Theory |
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35 | (3) |
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1.4.3 Probability as an Encoding of In formation |
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38 | (2) |
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1.4.4 A Hybrid Bayesian Solution |
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40 | (2) |
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1.4.5 Gambles, Odds, and Probability Measurement |
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42 | (3) |
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45 | (9) |
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1.5.1 Conditional Probabilities |
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45 | (2) |
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1.5.2 Conjunctive Events and Bayes Theorem |
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47 | (3) |
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1.5.3 Statistical Dependence and Independence |
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50 | (3) |
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1.5.4 Disjunctions from Conjunctions |
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53 | (1) |
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1.6 Probability Trees and Unlimited Games |
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54 | (3) |
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57 | (6) |
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63 | (90) |
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63 | (1) |
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2.2 Binomial Features and Examples |
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63 | (2) |
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2.2.1 Examples of Binomial Sampling |
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64 | (1) |
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2.3 Binomial Distribution |
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65 | (9) |
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2.3.1 Normal Approximation to the Binomial |
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71 | (2) |
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2.3.2 Binomial Model over Experiments |
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73 | (1) |
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2.4 Bayesian Inference---Discrete Approximation |
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74 | (9) |
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78 | (2) |
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2.4.2 Interval Estimation |
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80 | (2) |
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82 | (1) |
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2.4.4 Quality of the Discrete-Approach Model |
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83 | (1) |
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2.5 Bayesian Inference---Continuous Model |
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83 | (15) |
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2.5.1 The Beta Distribution and the Binomial Model |
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83 | (4) |
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2.5.2 Monte Carlo Samples from the Posterior Distribution |
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87 | (2) |
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2.5.3 Case Study Example: TAS2R38 Gene Study |
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89 | (2) |
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2.5.4 Case Study Example: Machine Recalibration Decision |
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91 | (2) |
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2.5.5 Bayesian-Sign Test: A Pattern-Recognition Case Study |
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93 | (5) |
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98 | (10) |
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2.6.1 The Fisher Invariance Principle and the Jeffreys Prior |
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98 | (5) |
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2.6.2 Uninformative versus Informative Priors |
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103 | (5) |
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2.7 Statistical Decisions and the Bayes Factor |
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108 | (12) |
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2.7.1 The Predictive Distribution and Sequential Sampling |
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109 | (2) |
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2.7.2 The Bayes Factor for Interval Hypotheses |
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111 | (3) |
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2.7.3 Bayes Factor for the Sharp Null Hypothesis |
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114 | (2) |
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2.7.4 Bayes Factor for a Trivially Small Null Interval |
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116 | (1) |
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2.7.5 Bayes Factors and Sample Size Planning |
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117 | (1) |
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2.7.6 Criticisms of the Bayes Factor |
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118 | (2) |
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2.8 Comparison to the Frequentist Analysis |
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120 | (25) |
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2.8.1 The Frequentist Maximum Likelihood Estimate |
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120 | (2) |
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2.8.2 Frequmtist Hypothesis Testing |
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122 | (7) |
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2.8.3 The Confidence Interval |
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129 | (5) |
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2.8.4 Power and Sample Size Planning |
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134 | (3) |
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2.8.5 Likelihood Principle |
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137 | (4) |
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2.8.6 Meta-Analysis Comparisons |
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141 | (4) |
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145 | (8) |
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153 | (56) |
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153 | (1) |
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3.2 Multinomial Distribution and Examples |
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153 | (6) |
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3.2.1 Examples of Multinomial Studies |
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154 | (1) |
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3.2.2 The Multinomial Distribution |
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155 | (4) |
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3.3 The Dirichlet Distribution |
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159 | (8) |
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3.3.1 Covariation of the Dirichlet Variables |
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163 | (4) |
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3.4 Random Samples from a Dirichlet Distribution |
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167 | (4) |
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3.5 Multinomial Process Models |
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171 | (8) |
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3.5.1 Logistic Models versus Latent Process Models |
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171 | (2) |
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3.5.2 Introduction to Two Process-Tree Models |
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173 | (1) |
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3.5.3 The Recall/2-AFC Follow-Up Model |
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174 | (2) |
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3.5.4 The Chechile-Soraci (1999) Model |
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176 | (3) |
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3.6 Markov Chain Monte Carlo Estimation |
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179 | (13) |
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3.6.1 Classic Monte Carlo Sampling |
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179 | (4) |
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3.6.2 Introduction to Markov Chain Monte Carlo |
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183 | (4) |
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3.6.3 MCMC Estimation for the Recall/2-AFC Model |
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187 | (4) |
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3.6.4 MCMC Estimation for the Chechile-Soraci Model |
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191 | (1) |
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3.7 Population Parameter Mapping |
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192 | (9) |
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3.7.1 PPM Estimation for the Recall/2-AFC Model |
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194 | (3) |
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3.7.2 PPM Estimation for the Chechile-Soraci Model |
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197 | (4) |
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201 | (3) |
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3.9 Appendix: Proofs of Selected Theorems |
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204 | (5) |
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4 Condition Effects: Categorical Data |
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209 | (70) |
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209 | (1) |
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4.2 The Importance of Comparison Conditions |
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210 | (1) |
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4.3 Related Contingency Tables (1 = 2 Conditions) |
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211 | (11) |
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4.3.1 The Classical McNemar Test |
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212 | (4) |
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4.3.2 Bayesian 2 × 2 RB-Contingency Tables (L = 2) |
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216 | (2) |
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4.3.3 Classical m × m RB-Contingency Tables (L = 2) |
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218 | (1) |
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4.3.4 Bayesian m × m RB-Contingency Tables (L = 2) |
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219 | (3) |
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4.4 Bayesian CR Analysis (L = 2 Conditions) |
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222 | (4) |
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4.4.1 CR (L = 2) Contingency Table Framework |
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222 | (1) |
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4.4.2 Bayesian (L = 2, k = 1) Contingency Table Analysis |
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223 | (2) |
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4.4.3 Bayesian (L = 2, k > 1) Contingency Table Analysis |
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225 | (1) |
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4.5 Multiple Comparisons for Bayesian Inference |
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226 | (22) |
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4.5.1 Contrasts and Frequentist Multiple Comparisons |
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226 | (6) |
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4.5.2 Multiple Comparisons from a Bayesian Perspective |
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232 | (10) |
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4.5.3 Examples of Bayesian Multiple Comparison Analyses |
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242 | (6) |
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4.6 L ≥ 2 Completely Randomized Conditions |
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248 | (7) |
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4.6.1 Frequentist Omnibus Test for Independence |
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248 | (2) |
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4.6.2 Pointlessness of the Chi-Square Independence Test |
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250 | (2) |
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4.6.3 Bayesian Analysis for L ≥ 2 Groups or Conditions |
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252 | (3) |
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4.7 L ≥ 2 Randomized-Block Conditions |
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255 | (8) |
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4.7.1 Binomial Data: Frequentist Test |
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258 | (1) |
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4.7.2 Bayesian RB-Contingency Tables for L ≥ 2: Binomial Data |
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259 | (1) |
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4.7.3 Bayesian RB Analysis for Multinomial Data with L ≥ 2 |
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260 | (3) |
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4.8 2 × 2 Split-Plot or Mixed Designs |
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263 | (2) |
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4.9 Planning the Sample Size in Advance |
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265 | (5) |
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4.9.1 Sample-Size Planning for RB Experiments |
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267 | (1) |
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4.9.2 Sample-Size Planning for CR Experiments |
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268 | (2) |
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4.10 Overview of Bayesian Comparison Procedures |
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270 | (2) |
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272 | (7) |
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II Bayesian Analysis of Ordinal Information |
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279 | (150) |
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5 Median- And Sign-Based Methods |
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285 | (32) |
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285 | (1) |
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285 | (13) |
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5.2.1 Examples of a Median Test Analysis |
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285 | (2) |
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5.2.2 Frequentist Median Test for L = 2 Groups |
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287 | (4) |
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5.2.3 Frequentist Median Test Extension for L > 2 |
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291 | (1) |
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5.2.4 Bayesian Median-Test Analysis L = 2 CR Conditions |
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292 | (2) |
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5.2.5 Bayesian Median-Test Analysts L > 2 Conditions |
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294 | (1) |
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5.2.6 Limitations of the Median Test |
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295 | (3) |
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5.3 Sign Test for RB Research Designs |
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298 | (7) |
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5.3.1 Bayesian L = 2 Conditions Sign Test |
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300 | (1) |
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5.3.2 Frequentist Tests for Rank-Based RB Designs for L > 2 |
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301 | (2) |
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5.3.3 Bayesian Multiple-Sign Tests for RB Designs for L > 2 |
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303 | (1) |
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5.3.4 Sample Size and the Bayes-Factor Relative Efficiency |
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304 | (1) |
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5.4 Bayesian Nonparametric Split-Plot Analysis |
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305 | (7) |
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312 | (5) |
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6 Wilcoxon Signed-Rank Procedure |
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317 | (24) |
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317 | (1) |
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6.2 Frequentist Wilcoxon Signed-Rank Analysis |
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317 | (4) |
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6.2.1 Examples for the Wilcoxon Signed-Rank Statistic |
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317 | (2) |
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6.2.2 Frequentist Wilcoxon Analysis |
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319 | (2) |
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6.3 Bayesian Discrete Small-Sample Analysis |
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321 | (7) |
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6.3.1 Introduction to Bayesian Wilcoxon Analysis |
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321 | (5) |
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6.3.2 Noninteger T+ for n < 25 |
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326 | (1) |
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6.3.3 Comparisons to the Yuan-Johnson Approach |
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327 | (1) |
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6.4 Continuous Large-Sample Model |
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328 | (6) |
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6.4.1 The Large-Sample Model |
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328 | (4) |
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6.4.2 A Meta-Analysis Application |
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332 | (2) |
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6.5 Comparisons with Other Procedures |
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334 | (3) |
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6.5.1 Comparisons with the Bayesian Sign Test |
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334 | (1) |
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6.5.2 Comparisons with the Within-Block t Test |
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335 | (2) |
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337 | (2) |
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6.7 Appendix: Discrete-Approximation Software |
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339 | (2) |
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341 | (30) |
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341 | (1) |
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7.2 Frequentist Mann-Whitney Statistic |
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341 | (6) |
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7.2.1 Some Examples for the Mann-Whitney Statistic |
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342 | (1) |
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7.2.2 The Mann-Whitney Statistics |
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343 | (4) |
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7.3 Bayesian Mann-Whitney Analysis: Discrete Case |
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347 | (8) |
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7.3.1 The Population Difference Proportion Parameter |
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347 | (1) |
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7.3.2 Exponential Mimicry and the Likelihood Function |
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348 | (4) |
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7.3.3 Discrete Small-Sample Analysis |
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352 | (3) |
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7.4 Continuous Larger-Sample Approximation |
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355 | (6) |
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355 | (4) |
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7.4.2 Stress-Strength Application |
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359 | (2) |
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7.5 Planning and Bayes-Factor Relative Efficiency |
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361 | (1) |
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7.6 Comparisons to the Independent-Groups t Test |
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362 | (1) |
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363 | (2) |
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7.8 Appendix: Programs and Documentation |
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365 | (6) |
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7.8.1 Program for the Discrete Approximation Method |
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365 | (1) |
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7.8.2 Lagrange Estimates for ΩE(x), na, and nb |
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366 | (5) |
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8 Distribution-Free Correlation |
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371 | (58) |
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371 | (1) |
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8.2 Introduction to Rank-Based Correlation |
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371 | (16) |
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8.2.1 Three Correlation Coefficients |
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373 | (14) |
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8.3 The Kendall Tau with Tied Ranks |
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387 | (8) |
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8.3.1 The Goodman-Kruskal G Statistic |
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391 | (4) |
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8.4 Bayesian Analysis for the Kendall Tau |
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395 | (19) |
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8.4.1 Study of Brain Size and Intelligence |
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403 | (1) |
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8.4.2 Predicting Consumer Preference |
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404 | (1) |
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8.4.3 Ordered-Contingency Table Application |
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405 | (2) |
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8.4.4 Monte Carlo Comparisons |
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407 | (3) |
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8.4.5 Kendall Tau and Experimental Differences |
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410 | (4) |
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8.5 Testing Theories with the Kendall Tau |
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414 | (12) |
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8.5.1 Comparing Scientific Functions |
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414 | (3) |
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8.5.2 Testing Theories of the Risky Weighting Function |
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417 | (4) |
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8.5.3 Testing for a Perfect or Near-Perfect Fit |
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421 | (5) |
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426 | (3) |
References |
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429 | (18) |
Index |
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447 | |