Preface |
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xi | |
1 Odds Ratio Parameter and Its Utilities |
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1 | (20) |
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1.1 Relative risk and odds ratio parameter |
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1 | (2) |
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1.2 Odds ratio parameters in a J x K contingency table |
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3 | (3) |
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1.3 Odds ratio representations of conditional and joint distributions for a J x K contingency table |
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6 | (1) |
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1.4 Maximum likelihood estimators of odds ratio parameters in a J x K contingency table |
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7 | (4) |
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1.5 Link to logit model and logistic regression |
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11 | (1) |
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1.6 Odds ratio parameters in stratified 2 x 2 tables |
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11 | (2) |
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1.7 Common odds ratio parameter |
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13 | (2) |
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1.8 Odds ratio representations for a J x K x M contingency table |
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15 | (3) |
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1.9 Summary and discussion |
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18 | (1) |
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19 | (2) |
2 Odds Ratio Function and Its Modeling |
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21 | (34) |
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21 | (1) |
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2.2 Odds ratio decomposition of density functions |
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22 | (5) |
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2.3 Odds ratio representation of densities |
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27 | (3) |
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2.4 Conditional odds ratio function |
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30 | (1) |
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2.5 Odds ratio representation of a joint conditional density |
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31 | (1) |
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2.6 Odds ratio representation of a complex joint density |
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32 | (3) |
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2.7 Relationship between conditional and unconditional odds ratio functions |
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35 | (2) |
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2.8 Hierarchical odds ratio representation for a joint density |
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37 | (3) |
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2.9 Odds ratio functions embedding in a density function |
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40 | (3) |
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2.10 Modeling odd ratio functions in a family of densities |
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43 | (3) |
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2.11 Semiparametric odds ratio model |
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46 | (2) |
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2.12 Extension to relax the positivity condition for the odds ratio representation |
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48 | (3) |
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2.13 Literature on odds ratio functions and relevant statistical models |
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51 | (1) |
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52 | (3) |
3 Estimation and Inference on Semiparametric Odds Ratio Model |
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55 | (32) |
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3.1 An introduction to likelihood-based approaches |
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55 | (1) |
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3.2 Pseudo-likelihood approaches |
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56 | (5) |
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3.2.1 Pairwise and group-wise pseudo-likelihood approaches |
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56 | (3) |
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3.2.2 Asymptotic theory for U-statistics |
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59 | (1) |
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3.2.3 Asymptotic distributions of the pseudo-likelihood estimators |
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60 | (1) |
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3.3 Permutation likelihood approach |
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61 | (9) |
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3.3.1 Approximations using simple Monte Carlo or asymptotics |
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62 | (2) |
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3.3.2 Adaptive Monte Carlo approximation to permutation likelihood |
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64 | (2) |
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3.3.3 Metropolis algorithm for sampling permutations for estimation |
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66 | (1) |
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3.3.4 Permutation likelihood for the joint model |
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67 | (3) |
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3.4 Maximum semiparametric likelihood approach |
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70 | (6) |
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3.4.1 Maximum likelihood estimator for one group of outcomes |
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70 | (1) |
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3.4.2 Computation of the maximum likelihood estimator |
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71 | (2) |
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3.4.3 Maximum likelihood estimator for two groups of outcomes |
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73 | (1) |
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3.4.4 Maximum likelihood for more than two groups of outcomes |
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74 | (1) |
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3.4.5 Large sample behavior of the maximum likelihood estimator |
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75 | (1) |
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3.5 Comparison of different likelihood approaches |
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76 | (1) |
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3.6 The R package SPORM for semiparametric odds ratio model |
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76 | (2) |
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3.7 Simulation study using SPORM |
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78 | (4) |
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78 | (2) |
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3.7.2 Multivariate outcomes as a group |
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80 | (1) |
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3.7.3 Multivariate outcomes |
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81 | (1) |
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3.8 Data analysis using SPORM |
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82 | (2) |
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84 | (3) |
4 Estimation and Inference on Conditional Odds Ratio Function |
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87 | (20) |
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4.1 A general formulation of the problem |
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87 | (1) |
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4.2 Permutation approach for stratified sample |
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88 | (4) |
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4.2.1 Permutation likelihood approach |
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88 | (2) |
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4.2.2 Application to common odds ratio estimation in stratified 2 x 2 tables |
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90 | (2) |
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4.3 Semiparametric efficient score for estimating conditional odds ratio function |
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92 | (3) |
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4.3.1 Characterization of the nuisance score space and its orthogonal complement |
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92 | (1) |
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4.3.2 The semiparametric efficient score |
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93 | (1) |
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4.3.3 Locally efficient estimator |
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94 | (1) |
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4.4 The special case with one categorical outcome |
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95 | (2) |
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4.5 Doubly robust estimation of conditional odds ratio function |
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97 | (5) |
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4.5.1 An alternative characterization of the orthogonal complement of the nuisance score space |
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98 | (1) |
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4.5.2 The doubly robust property |
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99 | (2) |
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4.5.3 A more specific case |
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101 | (1) |
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4.6 Robust estimation of conditional odds ratio function in multiple outcome models |
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102 | (2) |
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4.7 Summary and literature |
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104 | (1) |
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104 | (3) |
5 Application to Biased Sampling Problems |
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107 | (28) |
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5.1 The general biased sampling problem |
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107 | (2) |
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5.2 Parameter identifiability for outcome-dependent sample |
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109 | (6) |
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5.2.1 Identifiability of model components |
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109 | (1) |
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5.2.2 Parameter identifiability in case-control design |
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110 | (2) |
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5.2.3 Parameter identifiability in outcome-dependent sampling design |
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112 | (2) |
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5.2.4 Extreme-value sampling and length-biased sampling designs |
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114 | (1) |
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5.3 Outcome-dependent sampling designs with covariate matching |
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115 | (3) |
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5.3.1 The general framework |
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115 | (1) |
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5.3.2 Matched case-control design |
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116 | (1) |
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5.3.3 Extreme-value sampling design with matching |
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117 | (1) |
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5.4 Parameter estimation with biased sampling designs |
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118 | (3) |
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5.5 Analysis of misspecified odds ratio model |
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121 | (5) |
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5.5.1 Misspecification in the semiparametric odds ratio model |
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121 | (1) |
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5.5.2 The permutation likelihood approach under misspecified models |
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121 | (4) |
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5.5.3 The maximum semiparametric likelihood approach under misspecified model |
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125 | (1) |
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126 | (6) |
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5.6.1 Gene-environment independence in case-control genetic association study |
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126 | (2) |
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5.6.2 Secondary traits analysis in a case-control genetic association study |
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128 | (2) |
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5.6.3 Case-only design to study interactions |
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130 | (2) |
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5.7 Summary and literature |
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132 | (1) |
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133 | (2) |
6 Application to Test of Conditional Independence |
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135 | (34) |
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6.1 An introduction to test of conditional independence |
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135 | (1) |
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6.2 Likelihood ratio tests |
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136 | (3) |
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6.2.1 Prospective, retrospective, and joint likelihood ratio tests |
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136 | (2) |
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6.2.2 Likelihood ratio tests based on permutation likelihoods |
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138 | (1) |
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6.3 Likelihood score tests |
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139 | (7) |
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6.3.1 Prospective, retrospective, and joint likelihood score tests |
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139 | (5) |
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6.3.2 Permutation likelihood score tests |
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144 | (2) |
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6.4 Semiparametric efficient score test |
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146 | (4) |
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6.4.1 Semiparametric likelihood formulation |
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146 | (2) |
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6.4.2 Permutation likelihood formulation |
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148 | (2) |
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6.5 Doubly robust test of conditional independence |
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150 | (7) |
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6.5.1 Estimates based on the semiparametric likelihoods |
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150 | (3) |
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6.5.2 Permutation-based doubly robust test of independence |
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153 | (3) |
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6.5.3 Bootstrap implementation of the doubly robust tests |
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156 | (1) |
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6.6 Connections to classical tests of conditional independence |
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157 | (3) |
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6.7 Likelihood ratio test using the R package SPORM |
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160 | (2) |
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6.8 A simulation study of the doubly robust tests |
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162 | (3) |
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6.9 Summary and literature |
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165 | (1) |
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166 | (3) |
7 Application to Network Detection and Estimation |
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169 | (22) |
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7.1 Network and Gaussian graphical model |
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169 | (1) |
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7.2 Gaussian network detection approaches |
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170 | (4) |
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7.2.1 The neighborhood detection approach |
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170 | (1) |
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7.2.2 The joint detection approach |
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171 | (1) |
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7.2.3 The screening approach based on partial correlation coefficient |
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172 | (2) |
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7.3 Network modeling by the semiparametric odds ratio model |
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174 | (1) |
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7.4 Network detection by penalized likelihoods based on permutations |
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175 | (6) |
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7.4.1 Penalized pairwise pseudo-likelihood approach |
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175 | (2) |
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7.4.2 Penalized permutation likelihood approach |
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177 | (3) |
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7.4.3 Hybrid algorithm for increasing the computation speed and estimation efficiency |
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180 | (1) |
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7.5 Network detection by penalized semiparametric likelihood approach |
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181 | (3) |
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7.5.1 Penalized likelihood for neighborhood selection |
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181 | (2) |
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7.5.2 Algorithms for finding the maximum penalized likelihood estimator |
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183 | (1) |
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7.6 Network selection using package SPORM |
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184 | (1) |
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185 | (2) |
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7.8 Summary and literature |
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187 | (1) |
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188 | (3) |
8 Application to Missing Data Problems |
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191 | (26) |
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8.1 A brief introduction to the missing data problem |
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191 | (1) |
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8.2 The missing covariate problem in regression analysis |
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192 | (3) |
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8.2.1 Missing covariates in parametric regression |
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192 | (2) |
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8.2.2 Missing covariates in the Cox regression model |
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194 | (1) |
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8.3 Monte Carlo algorithm for the likelihood maximization |
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195 | (4) |
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8.3.1 The general formulation |
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195 | (2) |
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8.3.2 Application to parametric regression |
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197 | (2) |
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8.3.3 Application to Cox regression model |
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199 | (1) |
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8.4 Imputation approach to missing covariates |
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199 | (9) |
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8.4.1 A Bayesian framework |
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199 | (2) |
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8.4.2 Draw (γ, G) from the posterior under the consecutive conditional odds ratio models |
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201 | (4) |
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8.4.3 Draw (γp, G) from the posterior under the joint odds ratio model |
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205 | (3) |
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8.4.4 Draw α and θ from their posteriors |
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208 | (1) |
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8.5 Application to nonignorable missing data |
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208 | (6) |
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8.5.1 Nonparametric identifiability of the full data model with missing at random |
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208 | (1) |
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8.5.2 Nonparametric identifiability of the full data model with missing not at random |
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209 | (3) |
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8.5.3 Odd ratio model for the item-wise independent nonresponse data |
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212 | (2) |
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8.6 Summary and literature |
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214 | (1) |
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214 | (3) |
9 Other Applications |
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217 | (14) |
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9.1 Compatibility of conditionally specified models |
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217 | (8) |
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9.1.1 The compatibility problem |
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217 | (1) |
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9.1.2 Compatibility of conditional densities |
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218 | (4) |
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9.1.3 Modifications to incompatible conditionally specified models based on the joint model construction |
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222 | (3) |
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9.1.4 Summary and literature |
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225 | (1) |
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9.2 Semiparametric estimation of multivariate density |
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225 | (4) |
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9.2.1 The semiparametric odds ratio model for density estimation |
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225 | (2) |
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9.2.2 Smoothed estimators for the semiparametric density |
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227 | (2) |
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9.2.3 Summary and literature |
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229 | (1) |
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229 | (2) |
10 Theoretical Results on Estimation and Inference |
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231 | (46) |
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10.1 Variation independence in the joint odds ratio representation of a density |
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231 | (1) |
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10.2 The semiparametric efficient score for semiparametric odds ratio model |
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232 | (2) |
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10.3 Theoretical properties of the semiparametric maximum likelihood estimator |
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234 | (9) |
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10.4 Properties of the maximum penalized semiparametric likelihood estimator |
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243 | (25) |
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10.4.1 Settings for the analysis |
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243 | (2) |
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10.4.2 Theoretical properties of the penalized semiparametric likelihood estimator |
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245 | (5) |
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10.4.3 Supplemental lemmas for the proofs of main results |
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250 | (18) |
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10.5 Bounds for the permutation distribution |
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268 | (9) |
Bibliography |
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277 | (12) |
Index |
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289 | |