BIOMETRICS 1 Volume 61

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Report of the Co-Editors - 2004
Report of the Co-Editors 2004 Brian Cullis, Laurence Freedman, Mike Kenward, Xihong Lin	vii
PRESIDENTIAL ADDRESS
Biometry, Biometrics, Biostatistics, Bioinformatics, , Bio-X Geert Molenberghs	1
REGULAR ARTICLES
Tight Clustering: A Resampling-Based Approach for Identifying Stable and Tight Patterns in Data George C. Tseng, Wing H. Wong	10
Iterative Partial Least Squares with Right-Censored Data Analysis: A Comparison to Other Dimension Reduction Techniques Jie Huang, David Harrington	17
Wavelet Thresholding with Bayesian False Discovery Rate Control Mahlet G. Tadesse, Joseph G. Ibrahim, Marina Vannucci, Robert Gentleman	25
Model Evaluation and Spatial Interpolation by Bayesian Combination of Observations with Outputs from Numerical Models Montserrat Fuentes, Adrian E. Raftery	36
Modeling Association among Demographic Parameters in Analysis of Open Population CaptureRecapture Data William A. Link, Richard J. Barker	46
Genetic Susceptibility to Prostate, Breast, and Colorectal Cancer among Nordic Twins Stuart G. Baker, Paul Lichtenstein, Jaakko Kaprio, Niels Holm	55
A Flexible B-Spline Model for Multiple Longitudinal Biomarkers and Survival Elizabeth R. Brown, Joseph G. Ibrahim, Victor DeGruttola	64
Multiple Imputation for Model Checking: Completed-Data Plots with Missing and Latent Data Andrew Gelman, Iven Van Mechelen, Geert Verbeke, Daniel F. Heitjan, Michel Meulders	74
A Sample Size Formula for the Supremum Log-Rank Statistic Kevin Hasegawa Eng, Michael R. Kosorok	86
Survival Model Predictive Accuracy and ROC Curves Patrick J. Heagerty, Yingye Zheng	92
Two-Sample Tests for Comparing Intra-Individual Genetic Sequence Diversity between Populations Peter B. Gilbert, A. J. Rossini, Raj Shankarappa	106
Bayesian Adaptive Biased-Coin Designs for Clinical Trials with Normal Responses Anthony C. Atkinson, Atanu Biswas	118
Bayesian Inferences on Predictors of Conception Probabilities David B. Dunson, Joseph B. Stanford	126
Multi-List Methods Using Incomplete Lists in Closed Populations Jason Sutherland, Carl James Schwarz	134
A Markov Chain Model for Animal Estrous Cycling Data J. Zhai, R. W. Morris	141
Quantile Regression Models with Multivariate Failure Time Data Guosheng Yin, Jianwen Cai	151
Robust Estimation of Multivariate Covariance Components Amylou Dueck, Sharon Lohr	162
Semiparametric Estimation of Proportional Mean Residual Life Model in Presence of Censoring Y. Q. Chen, N. P. Jewell, X. Lei, S. C. Cheng	170
Bias-Corrected Maximum Likelihood Estimator of the Negative Binomial Dispersion Parameter Krishna Saha, Sudhir Paul	179
Genomic Control for Association Studies under Various Genetic Models Gang Zheng, Boris Freidlin, Zhaohai Li, Joseph L. Gastwirth	186
A Queueing Model for Chronic Recurrent Conditions under Panel Observation Catherine M. Crespi, William G. Cumberland, Sally Blower	193
A Stochastic Model to Analyze Clonal Data on Multi-Type Cell Populations Ollivier Hyrien, Margot Mayer-Pröschel, Mark Noble, Andrei Yakovlev	199
A Class of Bayesian Shared Gamma Frailty Models with Multivariate Failure Time Data Guosheng Yin, Joseph G. Ibrahim	208
Two-Dimensional Dose Finding in Discrete Dose Space Kai Wang, Anastasia Ivanova	217
Regression Modeling of Competing Risks Data Based on Pseudovalues of the Cumulative Incidence Function John P. Klein, Per Kragh Andersen	223
Bayesian Population Dynamics of Interacting Species: Great Gerbils and Fleas in Kazakhstan Arnoldo Frigessi, Marit Holden, Clare Marshall, Hildegunn Viljugrein, Nils Chr. Stenseth, Lars Holden, Vladimir Ageyev, Nikolay L. Klassovskiy	230
CONSULTANT'S FORUM
Bayesian Monitoring of Clinical Trials with Failure-Time Endpoints Gary L. Rosner	239
Attributable Effects in Case2-Studies Paul R. Rosenbaum	246
Comparison of Maximum Statistics for Hypothesis Testing When a Nuisance Parameter Is Present only under the Alternative Gang Zheng, Zehua Chen	254
Assessing Accuracy of Mammography in the Presence of Verification Bias and Intrareader Correlation Yingye Zheng, William E. Barlow, Gary Cutter	259
Closure Procedures for Monotone Bi-Factorial DoseResponse Designs M. Hellmich, W. Lehmacher	269
Multiplicity-Adjusted Inferences in Risk Assessment: Benchmark Analysis with Quantal Response Data Daniela K. Nitcheva, Walter W. Piegorsch, R. Webster West, Ralph L. Kodell	277
Extending McNemar's Test: Estimation and Inference When Paired Binary Outcome Data Are Misclassified Robert H. Lyles, John M. Williamson, Hung-Mo Lin, Charles M. Heilig	287
Applying Concepts of Generalizability Theory on Clinical Trial Data to Investigate Sources of Variation and Their Impact on Reliability Tony Vangeneugden, Annouschka Laenen, Helena Geys, Didier Renard, Geert Molenberghs	295
An Estimator for Treatment Comparisons among Survivors in Randomized Trials Douglas Hayden, Donna K. Pauler, David Schoenfeld	305

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REGULAR ARTICLES
Likelihood Methods for Treatment Noncompliance and Subsequent Nonresponse in Randomized Trials A. James O'Malley, Sharon-Lise T. Normand	325
Determining a Maximum-Tolerated Schedule of a Cytotoxic Agent Thomas M. Braun, Zheng Yuan, Peter F. Thall	335
A Bayesian Approach to Jointly Modeling Toxicity and Biomarker Expression in a Phase I/II Dose-Finding Trial B. Nebiyou Bekele, Yu Shen	343
Variance Estimation in Clinical Studies with Interim Sample Size Reestimation Frank Miller	355
Adaptive Design and Estimation in Randomized Clinical Trials with Correlated Observations Guosheng Yin, Yu Shen	362
Adaptive Risk Group Refinement Michael LeBlanc, James Moon, John Crowley	370
Partly Conditional Survival Models for Longitudinal Data Yingye Zheng, Patrick J. Heagerty	379
A General Class of Bayesian Survival Models with Zero and Nonzero Cure Fractions Guosheng Yin, Joseph G. Ibrahim	403
Effects of Variance-Function Misspecification in Analysis of Longitudinal Data You-Gan Wang, Xu Lin	413
Estimation of Breeding Values Using Selected Pedigree Records Richard Morton, Jordan M. Howarth	422
Estimating the Species Accumulation Curve Using Mixtures Chang Xuan Mao, Robert K. Colwell, Jing Chang	433
Multievent: An Extension of Multistate CaptureRecapture Models to Uncertain States Roger Pradel	442
Analyzing Multi-environment Variety Trials Using Randomization-Derived Mixed Models T. Caliski, S. Czajka, Z. Kaczmarek, P. Krajewski, W. Pilarczyk	448
A Semiparametric Two-Component "Compound" Mixture Model and Its Application to Estimating Malaria Attributable Fractions Jing Qin, Denis H. Y. Leung	456
A Likelihood Approach for Quantitative-Trait-Locus Mapping with Selected Pedigrees K. Wang	465
The Full EM Algorithm for the MLEs of QTL Effects and Positions and Their Estimated Variances in Multiple-Interval Mapping Zehua Chen	474
Statistical Aspects in Physical Mapping Application to the Genome of O. oeni Strain GM Luzia Gonçalves, Líbia Zé-Zé, Hildete Prisco Pinheiro, Maria Antónia Amaral-Turkman	481
Imputation and Variable Selection in Linear Regression Models with Missing Covariates Xiaowei Yang, Thomas R. Belin, W. John Boscardin	498
Variable Selection for Marginal Longitudinal Generalized Linear Models Eva Cantoni, Joanna Mills Flemming, Elvezio Ronchetti	507
Frequentist Performance of Bayesian Confidence Intervals for Comparing Proportions in 2 2 Contingency Tables Alan Agresti, Yongyi Min	515
Exact Two-Sample Inference with Missing Data Ying Kuen Cheung	524
Adjusting O'Brien's Test to Control Type I Error for the Generalized Nonparametric BehrensFisher Problem Peng Huang, Barbara C. Tilley, Robert F. Woolson, Stuart Lipsitz	532
CONSULTANT'S FORUM
Nonparametric Estimation of the Bivariate Recurrence Time Distribution Chiung-Yu Huang, Mei-Cheng Wang	392
Bayesian Error-in-Variable Survival Model for the Analysis of GeneChip Arrays Mahlet G. Tadesse, Joseph G. Ibrahim, Robert Gentleman, Sabina Chiaretti, Jerome Ritz, Robin Foa	488
Continuous Toxicity Monitoring in Phase II Trials in Oncology Anastasia Ivanova, Bahjat F. Qaqish, Michael J. Schell	540
A Note on P-Values under Group Sequential Testing and Nonproportional Hazards Daniel L. Gillen, Scott S. Emerson	546
Bayesian Cure Rate Frailty Models with Application to a Root Canal Therapy Study Guosheng Yin	552
Modeling Late Entry Bias in Survival Analysis Masaaki Matsuura, Shinto Eguchi	559
Semiparametric Analysis of Survival Data with Left Truncation and Dependent Right Censoring Hongyu Jiang, Jason P. Fine, Rick Chappell	567
A Varying-Coefficient Cox Model for the Effect of Age at a Marker Event on Age at Menopause Bin Nan, Xihong Lin, Lynda D. Lisabeth, Siobán D. Harlow	576
On a Supplemented CaseControl Design Ruth M. Pfeiffer, Nilanjan Chatterjee	584

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REGULAR ARTICLES
Capture–Recapture Studies Using Radio Telemetry with Premature Radio-Tag Failure Laura Cowen, Carl J. Schwarz	637
Models for Estimating Bayes Factors with Applications to Phylogeny and Tests of Monophyly Marc A. Suchard, Robert E. Weiss, Janet S. Sinsheimer	665
Generalized Linear Latent Variable Models for Repeated Measures of Spatially Correlated Multivariate Data J. Zhu, J. C. Eickhoff, P. Yan	674
Robust Estimating Functions and Bias Correction for Longitudinal Data Analysis You-Gan Wang, Xu Lin, Min Zhu	684
Robust Tests for Treatment Effects Based on Censored Recurrent Event Data Observed over Multiple Periods Richard J. Cook, Wei Wei, Grace Y. Yi	692
On Corrected Score Approach for Proportional Hazards Model with Covariate Measurement Error Xiao Song, Yijian Huang	702
Simultaneous Group Sequential Analysis of Rank-Based and Weighted Kaplan–Meier Tests for Paired Censored Survival Data Adin-Cristian Andrei, Susan Murray	715
Propensity Score Matching with Time-Dependent Covariates Bo Lu	721
A Semiparametric Mixture Model for Analyzing Clustered Competing Risks Data Malay Naskar, Kalyan Das, Joseph G. Ibrahim	729
Combining Multiple Comparisons and Modeling Techniques in Dose-Response Studies F. Bretz, J. C. Pinheiro, M. Branson	738
Retrospective Analysis of Sequential Dose-Finding Designs John O'Quigley	749
Quantitative Risk Assessment for Multivariate Continuous Outcomes with Application to Neurotoxicology: The Bivariate Case Zi-Fan Yu, Paul J. Catalano	757
Bayesian Analysis for Generalized Linear Models with Nonignorably Missing Covariates Lan Huang, Ming-Hui Chen, Joseph G. Ibrahim	767
Bayesian Inference for Stochastic Kinetic Models Using a Diffusion Approximation A. Golightly, D. J. Wilkinson	781
Semiparametric Methods for Mapping Quantitative Trait Loci with Censored Data Guoqing Diao, D. Y. Lin	789
Assessing the Skill of Yes/No Predictions William Briggs, David Ruppert	799
Smooth Tests for the Zero-Inflated Poisson Distribution Olivier Thas, J. C. W. Rayner	808
CONSULTANT'S FORUM
Stratified Analysis in Randomized Trials with Noncompliance Shigeyuki Matsui	816
A Longitudinal Measurement Error Model with a Semicontinuous Covariate Liang Li, Jun Shao, Mari Palta	824
On the Effect of Misclassification on Bias of Perfectly Measured Covariates in Regression John P. Buonaccorsi, Petter Laake, Marit B. Veierød	831
Missing Covariates in Longitudinal Data with Informative Dropouts: Bias Analysis and Inference Jason Roy, Xihong Lin	837
Standard Errors for Attributable Risk for Simple and Complex Sample Designs Barry I. Graubard, Thomas R. Fears	847
READER REACTION
Line Transect Sampling in Small and Large Regions Rachel M. Fewster, Jeffrey L. Laake, Stephen T. Buckland	856
Rejoinder to "Line Transect Sampling in Small and Large Regions" G. J. Melville, A. H. Welsh	859
Comments about Joint Modeling of Cluster Size and Binary and Continuous Subunit-Specific Outcomes Ralitza V. Gueorguieva	862
Rejoinder to "Comments about Joint Modeling of Cluster Size and Binary and Continuous Subunit-Specific Outcomes" Zhen Chen, David B. Dunson	866
The Performance of Mixture Models in Heterogeneous Closed Population Capture–Recapture Shirley Pledger	868
Rejoinder to "The Performance of Mixture Models in Heterogeneous Closed Population Capture-Recapture" Robert M. Dorazio, J. Andrew Royle	874
CORRESPONDENCE
Bias Adjustment in Bayesian Estimation of Bird Nest Age-Specific Survival Rates Jing Cao, Chong Z. He	877
Letter to the Editor Paul S. Albert	879
Rejoinder to the Letter to the Editor from P. S. Albert Weichung Joe Shih, Shou-En Lu, Yong Lin	880

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DISCUSSION PAPER
Statistical Issues Arising in the Women's Health Initiative Ross L. Prentice, Mary Pettinger, Garnet L. Anderson	899
Discussion on "Statistical Issues Arising in the Women's Health Initiative" Raymond J. Carroll	911
Discussion on "Statistical Issues Arising in the Women's Health Initiative" N. E. Day	912
Discussion on "Statistical Issues Arising in the Women's Health Initiative" David L. DeMets	914
Discussion on "Statistical Issues Arising in the Women's Health Initiative" David A. Freedman, Diana B. Petitti	918
Discussion on "Statistical Issues Arising in the Women's Health Initiative" Sander Greenland	920
Discussion on "Statistical Issues Arising in the Women's Health Initiative" Miguel A. Hernán, James M. Robins, Luis A. García Rodríguez	922
Discussion on "Statistical Issues Arising in the Women's Health Initiative" Duncan C. Thomas	930
Discussion on "Statistical Issues Arising in the Women's Health Initiative" Anastasios A. Tsiatis, Marie Davidian	933
REGULAR ARTICLES
The Evaluation of Treatment When Center-Specific Selection Criteria Vary with Respect to Patient Risk Elizabeth R. DeLong, Laura P. Coombs, T. Bruce Ferguson Jr., Eric D. Peterson	942
Generalized Hierarchical Multivariate CAR Models for Areal Data Xiaoping Jin, Bradley P. Carlin, Sudipto Banerjee	950
Doubly Robust Estimation in Missing Data and Causal Inference Models Heejung Bang, James M. Robins	962
Generalization of the Mantel–Haenszel Estimating Function for Sparse Clustered Binary Data Molin Wang, John M. Williamson	973
A Case-Cohort Design for Assessing Covariate Effects in Longitudinal Studies Ruth M. Pfeiffer, Louise Ryan, Augusto Litonjua, David Pee	982
Nonparametric Estimation of Asymptomatic Duration from a Randomized Prospective Cancer Screening Trial Yu Shen, Xuelin Huang	992
Goodness-of-Fit Methods for Generalized Linear Mixed Models Zhiying Pan, D. Y. Lin	1000
Modeling Animals' Behavioral Response by Markov Chain Models for Capture–Recapture Experiments Hsin-Chou Yang, Anne Chao	1010
Bayesian Inferences on Umbrella Orderings Chris Hans, David B. Dunson	1018
Subset Clustering of Binary Sequences, with an Application to Genomic Abnormality Data Peter D. Hoff	1027
Individual and Population Penalized Regression Splines for Accelerated Longitudinal Designs Jaroslaw Harezlak, Louise M. Ryan, Jay N. Giedd, Nicholas Lange	1037
The Cox Proportional Hazards Model with a Continuous Latent Variable Measured by Multiple Binary Indicators Klaus Larsen	1049
MLE and Bayesian Inference of Age-Dependent Sensitivity and Transition Probability in Periodic Screening Dongfeng Wu, Gary L. Rosner, Lyle Broemeling	1056
Time-Varying Functional Regression for Predicting Remaining Lifetime Distributions from Longitudinal Trajectories Hans-Georg Müller, Ying Zhang	1064
A Shared Response Model for Clustered Binary Data in Developmental Toxicity Studies Zhen Pang, Anthony Y. C. Kuk	1076
A Semiparametric Method for Estimating Population Size for Capture–Recapture Experiments with Random Covariates in Continuous Time Paul S. F. Yip, Hua-Zhen Lin, Liqun Xi	1085
CONSULTANT'S FORUM
Improving Removal-Based Estimates of Abundance by Sampling a Population of Spatially Distinct Subpopulations Robert M. Dorazio, Howard L. Jelks, Frank Jordan	1093
Counterfactual Links to the Proportion of Treatment Effect Explained by a Surrogate Marker Jeremy M. G. Taylor, Yue Wang, Rodolphe Thiébaut	1102
READER REACTION
Modeling the Dependence between the Number of Trials and the Success Probability in Binary Trials M. J. Faddy, D. M. Smith	1112
On Analyzing Circadian Rhythms Data Using Nonlinear Mixed Models with Harmonic Terms Paul S. Albert, Sally Hunsberger	1115
Rejoinder to "On Analyzing Circadian Rhythms Data Using Nonlinear Mixed Models with Harmonic Terms" Yuedong Wang, Chunlei Ke, Morton B. Brown	1122
Modification of the Computational Procedure in Parker and Bregman's Method of Calculating Sample Size from Matched Case–Control Studies with a Dichotomous Exposure Ilya Novikov, Bernice Oberman, Laurence Freedman	1123
Rejoinder to "Modification of the Computational Procedure in Parker and Bregman's Method of Calculating Sample Size from Matched Case–Control Studies with a Dichotomous Exposure" Robert A. Parker	1126