

Software

CGEN, an R packages based on work with Nilanjan Chatterjee and YiHau Chen for analyzing genetic data on casecontrol samples, with particular emphasis on novel methods for detecting GeneGene and GeneEnvironment interactions.

SAS Macro and Demonstrations For Estimating Usual Intake Distributions of Food and Associated IndividualLevel Predictors for DietDisease Relationships
This site is based on our work involving the estimation of the usual intake distributyion for nutrients and episodically consumed foods. In addition, we estimate individuallevel usual intake for use in regression calibration analysis of dietdisease relationships.

SAS Macro for Haplotype Analysis
The SAS macro HapReg implements the haplotypebased genetic association
analysis for casecontrol studies, using a flexible model for geneenvironment
association allowing haplotypes to be potentially related with environmental
exposures. The novel methodology is proposed by Chen, Chatterjee, and Carroll
(2007, Retrospective Analysis of HaplotypeBased CaseControl Studies Under a
Flexible Model for GeneEnvironment Association, under revision).

WaveletBased Functional Mixed Model Methodology, Windows
These are programs based upon the work of Jeffrey Morris and Raymond Carroll, 2006, Journal of the Royal Statistical Society, Series B, 68, 179199

MatLab and R Programs for Mixtures of Berkson and Classical Measurement Errors in the Nevada Test Site Study
These are programs based upon the work of Yehua Li, Annamaria Guolo, F. Owen Hoffman and Raymond J. Carroll. There are Bayesian and MonteCarlo EM programs for the analysis of these important radiation data.

MatLab Programs for Retrospective Gene Environment Interaction Studies
This program allows for populationbased casecontrol analysis of geneenvironment interaction studies. Our novel methodology leads to much more efficient estimation of risk and interaction parameters than does ordinary logistic regression.

Programs for GeneEnvironment Interactions in CaseControl Studies
Based on the 2005 paper in Biometrika by Nilanjan Chatterjee and Raymond Carroll, "Semiparametric Maximum Likelihood Estimation in CaseControl Studies of GeneEnviroment Interactions". A generalization of the this work to account for haplotypes is in HapReg described above.

Programs called in the Measurement Error Short Course at ENAR, 2008
These are Stata, R2WinBUGS and some SAS Code for our measurement error short course.

MatLab
The following programs are in zipped directories. The various utility directories need to be unzipped since some of the functions call them.

Raymond Carroll's Utility Directory
Directory is called "carroll_utilities_directory"

David Ruppert's Utility Functions
Directory is called "utility".

SIMEX and Bayes Programs for Gaussian and Logistic Regression in the Instrumental Variables Problem
Uses regression splines. The set of programs is selfcontained, i.e., call no other of my directories. Based on a paper Nonlinear and Nonparametric Regression and Instrumental Variables by Raymond J. Carroll, David Ruppert, Ciprian M. Crainiceanu, Tor D. Tosteson and Margaret R. Karagas.

SIMEX and Bayes Programs for Gaussian Regression (linear link) with classical measurement error
The README files described which directories to call, namely the "carroll_modified_spline_functions" and "carroll_utilities_directory". Based on the paper Bayesian smoothing and regression splines for measurement error problems by S. Berry, R. J. Carroll and D. Ruppert, JASA, 97, 160169.

Spline and Kernel Methods for Longitudinal Data (Panel structure, linear link)
Directory is called "panel_data_directory". Computes regression spline estimators using GLS and working independence, and twostage kernel estimators. Based on the paper Linton, O. B., Mammen, E., Lin, X. & Carroll, R. J. (2003). Accounting for correlation in marginal longitudinal nonparametric regression. Second Seattle Symposium on Biostatistics, editor D. Lin. You must call the directories "srs", "lpoly", "ebbs", "utility".

Carroll Regression Spline Functions that have nothing to do with measurement error
Directory is called "carroll_modified_spline_functions"

Programs for local polynominal regression with bandwidth estimated from EBBS (A David Ruppert method)
Directory is called "ebbs".

Programs for spline regression that combine some of mine with some of David Ruppert's
Directory is called "srs".

Programs for local polynomial regression that combine some of mine with some of David Ruppert's
Directory is called "lpoly".

Programs for Bayesian fitting of adaptive Psplines in regression
Directory is called "adaptive_psplinesv06". You must call the directories "srs", "lpoly", "ebbs", "utility".

Programs for nonparametric regression in clustered data binning
Programs are selfcontained, i.e., call no other directories. Based upon the paper A Simple, General Approach To Inference In Mixed Parametric And Semiparametric Models by R. J. Carroll, P. Hall, T. V. Apanasovich and X. Lin.

Programs for analysis of matched casecontrol data with missing observations
Based on the paper Semiparametric Bayesian Analysis of Matched CaseControl Studies with Missing Exposure by S. Sinha, B. Mukherjee, M. Ghosh, B. K. Mallick and R. J. Carroll

Taylex and Other Deconvolution Programs
This implements the Taylex method of Carroll and Hall, JRSSB, 2004, volume 66, pages 3146. Calls utility, loply, ebbs and carroll_utilities.

John Staudenmeyer's programs for SIMEX in nonparametric regression with efficient bandwidth estimation
Based on the paper Staudenmeyer, J. and Ruppert, D. (2003). Local polynomial regression and SIMEX.

R programs
The R programs are basically translations of the MATLAB Programs. They are all in one directory.

R programs, zip file
Directory is called "R_programs"

CatReg

XploRe
  