Physical Sciences and Mathematics Commons^™

Site- And Location-Adjusted Approaches To Adaptive Allocation Clinical Trial Designs, Brian S. Di Pace

Theses and Dissertations

Response-Adaptive (RA) designs are used to adaptively allocate patients in clinical trials. These methods have been generalized to include Covariate-Adjusted Response-Adaptive (CARA) designs, which adjust treatment assignments for a set of covariates while maintaining features of the RA designs. Challenges may arise in multi-center trials if differential treatment responses and/or effects among sites exist. We propose Site-Adjusted Response-Adaptive (SARA) approaches to account for inter-center variability in treatment response and/or effectiveness, including either a fixed site effect or both random site and treatment-by-site interaction effects to calculate conditional probabilities. These success probabilities are used to update assignment probabilities for allocating patients …

Penalized Mixed-Effects Ordinal Response Models For High-Dimensional Genomic Data In Twins And Families, Amanda E. Gentry

Theses and Dissertations

The Brisbane Longitudinal Twin Study (BLTS) was being conducted in Australia and was funded by the US National Institute on Drug Abuse (NIDA). Adolescent twins were sampled as a part of this study and surveyed about their substance use as part of the Pathways to Cannabis Use, Abuse and Dependence project. The methods developed in this dissertation were designed for the purpose of analyzing a subset of the Pathways data that includes demographics, cannabis use metrics, personality measures, and imputed genotypes (SNPs) for 493 complete twin pairs (986 subjects.) The primary goal was to determine what combination of SNPs and …

Multiple Testing Correction With Repeated Correlated Outcomes: Applications To Epigenetics, Katie Leap

Masters Theses

Epigenetic changes (specifically DNA methylation) have been associated with adverse health outcomes; however, unlike genetic markers that are fixed over the lifetime of an individual, methylation can change. Given that there are a large number of methylation sites, measuring them repeatedly introduces multiple testing problems beyond those that exist in a static genetic context. Using simulations of epigenetic data, we considered different methods of controlling the false discovery rate. We considered several underlying associations between an exposure and methylation over time.

We found that testing each site with a linear mixed effects model and then controlling the false discovery rate …

Learning From Data: Plant Breeding Applications Of Machine Learning, Alencar Xavier

Open Access Dissertations

Increasingly, new sources of data are being incorporated into plant breeding pipelines. Enormous amounts of data from field phenomics and genotyping technologies places data mining and analysis into a completely different level that is challenging from practical and theoretical standpoints. Intelligent decision-making relies on our capability of extracting from data useful information that may help us to achieve our goals more efficiently. Many plant breeders, agronomists and geneticists perform analyses without knowing relevant underlying assumptions, strengths or pitfalls of the employed methods. The study endeavors to assess statistical learning properties and plant breeding applications of supervised and unsupervised machine learning …

Assessing The Effect Of Wal-Mart In Rural Utah Areas, Angela Nelson

Theses and Dissertations

Walmart and other “big box” stores seek to expand in rural markets, possibly due to cheap land and lack of zoning laws. In August 2000, Walmart opened a store in Ephraim, a small rural town in central Utah. It is of interest to understand how Walmart's entrance into the local market changes the sales tax revenue base for Ephraim and for the surrounding municipalities. It is thought that small “Mom and Pop” stores go out of business because they cannot compete with Walmart's prices, leading to a decrease in variety, selection, convenience, and most importantly, sales tax revenue base in …

Performance Of The Kenward-Project When The Covariance Structure Is Selected Using Aic And Bic, Elisa Valderas Gomez

Theses and Dissertations

Linear mixed models are frequently used to analyze data with random effects and/or repeated measures. A common approach to such analyses requires choosing a covariance structure. Information criteria, such as AIC and BIC, are often used by statisticians to help with this task. However, these criteria do not always point to the true covariance structure and therefore the wrong covariance structure is sometimes chosen. Once this step is complete, Wald statistics are used to test fixed effects. Degrees of freedom for these statistics are not known. However, there are approximation methods, such as Kenward and Roger (KR) and Satterthwaite (SW) …