Multiple Comparisons Using R

betty

目录
List of Tables xi
Preface xiii
1 Introduction 1
2 General Concepts 11
2.1 Error rates and general concepts 11
2.1.1 Error rates 11
2.1.2 General concepts 17
2.2 Construction methods 20
2.2.1 Union intersection test 20
2.2.2 Intersection union test 22
2.2.3 Closure principle 23
2.2.4 Partitioning principle 29
2.3 Methods based on Bonferroni's inequality 31
2.3.1 Bonferroni test 31
2.3.2 Holm procedure 32
2.3.3 Further topics 34
2.4 Methods based on Simes' inequality 35
3 Multiple Comparisons in Parametric Models 41
3.1 General linear models 41
3.1.1 Multiple comparisons in linear models 41
3.1.2 The linear regression example revisited using R 45
3.2 Extensions to general parametric models 48
3.2.1 Asymptotic results 48
3.2.2 Multiple comparisons in general parametric models 50
3.2.3 Applications 52
3.3 The multcomp package 53
3.3.1 The glht function 53
3.3.2 The summary method 59
3.3.3 The confint method 64
vii
© 2011 by Taylor and Francis Group, LLC
viii CONTENTS
4 Applications 69
4.1 Multiple comparisons with a control 70
4.1.1 Dunnett test 71
4.1.2 Step-down Dunnett test procedure 77
4.2 All pairwise comparisons 82
4.2.1 Tukey test 82
4.2.2 Closed Tukey test procedure 93
4.3 Dose response analyses 99
4.3.1 A dose response study on litter weight in mice 100
4.3.2 Trend tests 103
4.4 Variable selection in regression models 108
4.5 Simultaneous condence bands 111
4.6 Multiple comparisons under heteroscedasticity 114
4.7 Multiple comparisons in logistic regression models 118
4.8 Multiple comparisons in survival models 124
4.9 Multiple comparisons in mixed-eects models 125
5 Further Topics 127
5.1 Resampling-based multiple comparison procedures 127
5.1.1 Permutation methods 127
5.1.2 Using R for permutation multiple testing 137
5.1.3 Bootstrap testing { Brief overview 140
5.2 Group sequential and adaptive designs 140
5.2.1 Group sequential designs 141
5.2.2 Adaptive designs 150
5.3 Combining multiple comparisons with modeling 156
5.3.1 MCP-Mod: Dose response analyses under model uncertainty
157
5.3.2 A dose response example 162
Bibliography 167
Index 183

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