Quantitative Methods for HIV/AIDS Research

PrefaceSection I Quantitative Methods for Clinical Trials and EpidemiologyStatistical Issues in HIV Non-Inferiority TrialsIntroductionMargin of Non-InferiorityAnalysis of NI TrialsSample Size DeterminationOther Considerations in NI TrialsNoncomplianceMissing DataMisclassification and Measurement Error in Outcome VariablesSummaryReferencesSample Size for HIV-1 Vaccine Clinical Trials with Extremely Low Incidence RateIntroductionSample Size DeterminationPower AnalysisPrecision AnalysisRemarksChow and Chiu's Procedure for Sample Size EstimationSensitivity AnalysisAn ExampleData Safety Monitoring ProcedureConcluding RemarksReferencesAdaptive Clinical Trial DesignIntroductionDefinition of Adaptive DesignTypes of Adaptive DesignAdaptive Randomization DesignAdaptive Group Sequential DesignFlexible Sample Size Re-Estimation DesignDrop-the-Losers DesignAdaptive Dose-Finding DesignBiomarker-Adaptive DesignUtilization of Bayesian MethodsBenefits and Limitations of Adaptive DesignPossible BenefitsLimitationsRegulatory and Statistical ConcernsApplication of HIV-1 Vaccine TrialsConcluding RemarksReferencesGeneralizing Evidence from HIV Trials Using Inverse Probability of Sampling WeightsIntroductionBackgroundPublic Health ExamplesSampling Score Methods to Generalize Trial ResultsOverviewAssumptions and NotationInference about Population Treatment EffectsNo CensoringRight-Censored DataSimulationsApplicationsCohort and Trial DataAnalysisResultsDiscussionAcknowledgmentsReferencesStatistical Tests of Regularity among Groups with HIV Self-Test DataIntroductionStatistical BackgroundModelHypothesis Testing for RegularityIdentifiability of Model ParametersLR Tests for Uniformity One-Sample ProblemTwo-Sample ProblemApplication to a Study of Self-Testing for HIVSimulation StudiesDiscussionAcknowledgmentsReferencesSection II Quantitative Methods for Analysis of Laboratory AssaysEstimating Partial Correlations between Logged HIV RNA Measurements Subject to Detection LimitsIntroductionMethodsBasic Modeling Framework for Estimating the Partial CorrelationLikelihood-Based Methods for Bivariate Data Incorporating Covariates and NondetectablesMaximum Likelihood Method 1: A Conditional BVN ModelConfidence Intervals for the Partial Correlation Coefficient under ML Method 1ML Method 2: Univariate Normal Models Ignoring Records with Nondetectables on XPartial Regression Coefficient EstimationAlternative Univariate Models Adjusting for CovariatesMixture of Two Normal ModelsMixture Model Assuming a Point Mass below the LODPartial Correlation and Regression Coefficient Estimation under Alternative ModelsExample HERS DataHERS Example: Crude and Partial Correlation EstimatesHERS Example: Partial Regression Coefficient EstimatesHERS Example: Relative Fit of Candidate Univariate ModelsSimulation Study Evaluating Partial Correlation EstimatorsEvaluating Partial Regression Coefficient EstimatorsEvaluating Partial Regression Coefficient Estimators under Mixture Model for X|CDiscussionAcknowledgmentsReferencesQuantitative Methods and Bayesian Models for Flow Cytometry Analysis in HIV/AIDS ResearchFlow Cytometry in HIV/AIDS ResearchBrief Review of Automated AnalysisIntroduction to Bayesian ModelingBayesian Models for Cell Subset IdentificationFinite Gaussian Mixture ModelsDirichlet Process ModelsHierarchical Dirichlet Process ModelsBayesian Models for Comparative Analysis of Count DataConcluding RemarksReferencesThe Immunoglobulin Variable-Region Gene Repertoire and Its AnalysisIntroductionAntibodiesB-Cell DevelopmentDevelopment of the IgVRG Ig RepertoireAffinity MaturationB-Cell Response KineticsIgVRG Repertoire SequencingBroadly Neutralizing Antibodies against HIVFunctional and Genetic Characteristics of BNAbsAnalysis of IgVRG RepertoiresStochastic Generative Models for VDJ Recombination and Affinity MaturationInference of the FounderInference of the Founder from a Clonal AlignmentDetermination of Clonal KinshipClonal PartitioningSoftware AvailabilityAcknowledgmentsReferencesProbability-Scale Residuals in HIV/AIDS Research: Diagnostics and InferenceIntroductionProbability-Scale ResidualModel DiagnosticsStage of Cervical Lesions: Proportional Odds ModelsBiomarker Study of Metabolomics: Semiparametric Transformation ModelsInferenceTests of Residual CorrelationSpearman's Partial and Conditional Rank CorrelationsCovariance of PSRsExamplesStage of Cervical LesionsBiomarker Study of MetabolomicsGenome-Wide Association StudyDiscussionAcknowledgmentsReferencesSimulation Modeling of HIV Infection—From Individuals to Risk Groups and Entire PopulationsIntroduction in human populations. It is not intended to be a comprehensive review of the models (which are numerous) but rather a description of majorModeling MethodologyStatistical ModelsState Transition and Markov ModelsSystem DynamicsIndividual-Based (Microsimulation, Agent-Based) Models and Synthetic PopulationsSynthetic PopulationsFuture Population ProjectionsUncertainty in Simulation ModelsThe Use of Simulation Models in ForecastingModel Parameterization, Calibration, and ValidationModeling Applications to HIV Research Problems Within-Person HIV DynamicsIndividual Behavior RisksRisk GroupsPopulation ModelsDiscussionAcknowledgmentsReferencesReview of Statistical Methods for Within-Host HIV Dynamics in AIDS StudiesIntroductionOrdinary Differential Equations Modeling HIV InfectionModeling Drug EfficacyModeling Drug ResistanceModel IdentifiabilityPractical Identifiability AnalysisMonte Carlo SimulationCorrelation MatrixSensitivity-Based Identifiability AnalysisODE Model Fitting MethodsLeast Squares ApproachesHierarchical Modeling ApproachesSmoothing-Based ApproachesHigh-Dimensional ODE ModelingDiscussionReferencesPrecision in the Specification of Ordinary Differential Equations and Parameter Estimation in Modeling Biological ProcessesIntroductionModel Mis-Specification and Statistical Model ComparisonModel Parameter Identifiability and Study DesignThe Sensitivity MatrixTheFIMExamplesDiscussionReferences
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