BRIAN S CAFFO
Research Papers Seminars Software / Computing

Research Summary 

Papers
Manuscript
Topics


Jointly Modeling Continous and Binary Outcomes for Boolean Outcomes: An Application to Modeling Hypertension GLMMs / sleep


On the Merrits of Voxel Based Mophometric Path Analysis for Investigating Volumetric Mediation of a Toxicant's Effect of Cognitive Function MRI / neuroimaging


An Overview of Observational Sleep Research With Application to Sleep Transitioning Sleep


Relations of Brain Volumes With Cognitive Function in Males 45 Years and Older With Past Lead Exposure (with Schwartz et al.) MRI / neuroimaging
paper
A New Method to Quantitatively Estimate Seminal Vesicle and Prostate Gland Contributions to Ejaculate (with Hendrix et al.) Pharmacology
paper
A Case Study in Pharmacologic Imaging Using Principal Curves in
  Single Photon Emission Computed Tomography (with Crainiceanu et al.)
 SPECT/ Imaging code

Is MRI Based Volume a Mediator of the Association  of Cumulative Lead Dose With Cognitive Function (with Schwartze et al.) MRI / epidemiology
paper
A Bayesian Hierarchical Framework for Spatial Modeling of fMRI Data (with Bowman et al.) fMRI / Alzheimer's code
paper
Novel Methods in the Visualization of Transition Phenomena  (with Swihart et al.) Graphing/ Visualization  code

Modified Test Statistics by Inter-Voxel Variance Shrinkage With an Application to fMRI  (with Su et al.) fMRI / multilevel models


Accounting for Within Patient Correlation in Assessing Relative Sensitivity of an Adjunctive Diagnostic Test: Application to Lung Cancer (with Ryea and Scharfstein) Diagnostic testing
paper
Are Multilevel Models Helpful in Screening for Differentially Expressed Genes? (with Lu and Parmigiani) genomics / multilevel models


A Mechanistic Latent Variable Model for Estimating Drug Concentrations in the Male Genital Tract (with Choi et al.) Pharmacology / multilevel models
paper
A Survey of the Likelihood Approach to Bioequivalence (with Choi and Rohde) Pharmacology / likelihood methods


On the Potential for Ill-logic With Logically Defined Outcomes  (with Li and Scharfstein) Logical outcomes
paper
Optimal Sampling Times in Bioequivalence Studies Using a Simulated Annealing Algorithm (with Choi and Rohde) Pharmacology / computing
paper
Flexible Random Intercept Models for Binary Outcomes Using Mixtures of Normals (with An and Rohde) GLMMs /computing code paper notes
A New Method to Quantitatively Estimate Seminal Vesicle and Prostate Gland Contributions to Ejaculate (with Hendrix et al.) Pharmacology
paper
Cigarette Smoking and Sleep Disruption: Results from the Sleep Heart Health Study (with Punjabi et al.) Sleep
paper
Split Ejaculate Estimates of Seminal Vesicle and Prostate Gland Marker Concentrations (with Hendrix et al.) Pharmacology
paper
Fixed-width Output Analysis for Markov Chain Monte Carlo (with Jones et al.) MCMC
paper
A User-friendly Tutorial on Link-probit-normal Models (with Griswold) GLMMs / computing code paper
Exact Hypothesis Tests for Log-linear Models with exactLoglinTest Exact testing / computing / MCMC / Monte Carlo code paper notes
Familial Risk for Alzheimer’s Disease Alters fMRI Activation Patterns: A Study of Asymptomatic Offspring (with Bassett et al.) fMRI / Alzheimer's
paper
Ascent-based MCEM (with Jank and Jones) EM / Monte Carlo / computing code paper
Examples in which Misspecification of a Random Effects Distribution Reduces Efficiency, and Possible Remedies (with Agresti and Ohman) GLMMs / computing
paper
Monte Carlo Conditional Inference for Log-linear and Logistic Models: Survey of Current Methodology (with Booth) Exact testing / Monte Carlo / computing
paper
Simulation-Based P Values: Response to North et al. (with Broman) P-value calculations / Monte Carlo
paper
Empirical Sup Rejection Sampling (with Booth and Davison) Monte Carlo / computing
paper
Unequal Sampling for Monte Carlo EM Algorithms (with Booth) EM /  Monte Carlo / computing
paper
Measures of Relative Model Fit (with Agresti) Likelihood / computing
paper
Multinominal Logit Random Effect Models (with Agresti and Hartzel) GLMMs / computing
paper
A Markov Chain Monte Carlo Algorithm for Approximating Exact Conditional Probabilities (with Booth) Exact testing / MCMC / computing
paper
Simple and Effective Confidence Intervals for Proportions and Differences of Proportions Result from Adding Two Successes and Two Failures (with Agresti) Confidence intervals
paper
Random Effects Models for Categorical  Data (with Agresti et al.) GLMMs / computing
paper


Software / code
Exact loglin test R package
binary GLMM, code for fitting various kinds of binary GLMM models R package Sample code
powerConjugate, code for fitting various conjugacy models R package
Install notes for UbuntuNotes
ProcessGUI, software for image processing of 2D DICOM filesWebpage

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Seminars
Sleep log-linear JSM 2007
SPECT colon imaging UMBC 2007University of Florida 2007, Minnesota 2007
fMRI Alzheimer's disease UW CSSS 2007University of Florida 2007
Biosignals working group 2007 student recruitment visit
lead MRI volumetry 2006 student recruitment visit, 2007 MICE, biosignals 2006
Exact testing talk Samsi 2003,  JSM 2003
Empirical Bayes / gene expression JSM 2002,  Minnesota 2004
Split ejaculate methods 2005 talk  given to the dean
Ascent based MCEM  Talk
Environmental statistics talk given in 04 on Missing data Talk
ESUP talk JH 2002 and Duke 2003
Defense talk 2001 talk