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Missing data are common in psychology research and can lead to bias and reduced power if not properly handled. Multiple imputation is a state-of-the-art missing data method recommended by methodologists. Multiple imputation methods can generally be divided into two broad categories: joint model (JM) imputation and fully conditional specification (FCS)

Missing data are common in psychology research and can lead to bias and reduced power if not properly handled. Multiple imputation is a state-of-the-art missing data method recommended by methodologists. Multiple imputation methods can generally be divided into two broad categories: joint model (JM) imputation and fully conditional specification (FCS) imputation. JM draws missing values simultaneously for all incomplete variables using a multivariate distribution (e.g., multivariate normal). FCS, on the other hand, imputes variables one at a time, drawing missing values from a series of univariate distributions. In the single-level context, these two approaches have been shown to be equivalent with multivariate normal data. However, less is known about the similarities and differences of these two approaches with multilevel data, and the methodological literature provides no insight into the situations under which the approaches would produce identical results. This document examined five multilevel multiple imputation approaches (three JM methods and two FCS methods) that have been proposed in the literature. An analytic section shows that only two of the methods (one JM method and one FCS method) used imputation models equivalent to a two-level joint population model that contained random intercepts and different associations across levels. The other three methods employed imputation models that differed from the population model primarily in their ability to preserve distinct level-1 and level-2 covariances. I verified the analytic work with computer simulations, and the simulation results also showed that imputation models that failed to preserve level-specific covariances produced biased estimates. The studies also highlighted conditions that exacerbated the amount of bias produced (e.g., bias was greater for conditions with small cluster sizes). The analytic work and simulations lead to a number of practical recommendations for researchers.
ContributorsMistler, Stephen (Author) / Enders, Craig K. (Thesis advisor) / Aiken, Leona (Committee member) / Levy, Roy (Committee member) / West, Stephen G. (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Coarsely grouped counts or frequencies are commonly used in the behavioral sciences. Grouped count and grouped frequency (GCGF) that are used as outcome variables often violate the assumptions of linear regression as well as models designed for categorical outcomes; there is no analytic model that is designed specifically to accommodate

Coarsely grouped counts or frequencies are commonly used in the behavioral sciences. Grouped count and grouped frequency (GCGF) that are used as outcome variables often violate the assumptions of linear regression as well as models designed for categorical outcomes; there is no analytic model that is designed specifically to accommodate GCGF outcomes. The purpose of this dissertation was to compare the statistical performance of four regression models (linear regression, Poisson regression, ordinal logistic regression, and beta regression) that can be used when the outcome is a GCGF variable. A simulation study was used to determine the power, type I error, and confidence interval (CI) coverage rates for these models under different conditions. Mean structure, variance structure, effect size, continuous or binary predictor, and sample size were included in the factorial design. Mean structures reflected either a linear relationship or an exponential relationship between the predictor and the outcome. Variance structures reflected homoscedastic (as in linear regression), heteroscedastic (monotonically increasing) or heteroscedastic (increasing then decreasing) variance. Small to medium, large, and very large effect sizes were examined. Sample sizes were 100, 200, 500, and 1000. Results of the simulation study showed that ordinal logistic regression produced type I error, statistical power, and CI coverage rates that were consistently within acceptable limits. Linear regression produced type I error and statistical power that were within acceptable limits, but CI coverage was too low for several conditions important to the analysis of counts and frequencies. Poisson regression and beta regression displayed inflated type I error, low statistical power, and low CI coverage rates for nearly all conditions. All models produced unbiased estimates of the regression coefficient. Based on the statistical performance of the four models, ordinal logistic regression seems to be the preferred method for analyzing GCGF outcomes. Linear regression also performed well, but CI coverage was too low for conditions with an exponential mean structure and/or heteroscedastic variance. Some aspects of model prediction, such as model fit, were not assessed here; more research is necessary to determine which statistical model best captures the unique properties of GCGF outcomes.
ContributorsCoxe, Stefany (Author) / Aiken, Leona S. (Thesis advisor) / West, Stephen G. (Thesis advisor) / Mackinnon, David P (Committee member) / Reiser, Mark R. (Committee member) / Arizona State University (Publisher)
Created2012
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Description
Researchers are often interested in estimating interactions in multilevel models, but many researchers assume that the same procedures and interpretations for interactions in single-level models apply to multilevel models. However, estimating interactions in multilevel models is much more complex than in single-level models. Because uncentered (RAS) or grand

Researchers are often interested in estimating interactions in multilevel models, but many researchers assume that the same procedures and interpretations for interactions in single-level models apply to multilevel models. However, estimating interactions in multilevel models is much more complex than in single-level models. Because uncentered (RAS) or grand mean centered (CGM) level-1 predictors in two-level models contain two sources of variability (i.e., within-cluster variability and between-cluster variability), interactions involving RAS or CGM level-1 predictors also contain more than one source of variability. In this Master’s thesis, I use simulations to demonstrate that ignoring the four sources of variability in a total level-1 interaction effect can lead to erroneous conclusions. I explain how to parse a total level-1 interaction effect into four specific interaction effects, derive equivalencies between CGM and centering within context (CWC) for this model, and describe how the interpretations of the fixed effects change under CGM and CWC. Finally, I provide an empirical example using diary data collected from working adults with chronic pain.
ContributorsMazza, Gina L (Author) / Enders, Craig K. (Thesis advisor) / Aiken, Leona S. (Thesis advisor) / West, Stephen G. (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Understanding how adherence affects outcomes is crucial when developing and assigning interventions. However, interventions are often evaluated by conducting randomized experiments and estimating intent-to-treat effects, which ignore actual treatment received. Dose-response effects can supplement intent-to-treat effects when participants are offered the full dose but many only receive a

Understanding how adherence affects outcomes is crucial when developing and assigning interventions. However, interventions are often evaluated by conducting randomized experiments and estimating intent-to-treat effects, which ignore actual treatment received. Dose-response effects can supplement intent-to-treat effects when participants are offered the full dose but many only receive a partial dose due to nonadherence. Using these data, we can estimate the magnitude of the treatment effect at different levels of adherence, which serve as a proxy for different levels of treatment. In this dissertation, I conducted Monte Carlo simulations to evaluate when linear dose-response effects can be accurately and precisely estimated in randomized experiments comparing a no-treatment control condition to a treatment condition with partial adherence. Specifically, I evaluated the performance of confounder adjustment and instrumental variable methods when their assumptions were met (Study 1) and when their assumptions were violated (Study 2). In Study 1, the confounder adjustment and instrumental variable methods provided unbiased estimates of the dose-response effect across sample sizes (200, 500, 2,000) and adherence distributions (uniform, right skewed, left skewed). The adherence distribution affected power for the instrumental variable method. In Study 2, the confounder adjustment method provided unbiased or minimally biased estimates of the dose-response effect under no or weak (but not moderate or strong) unobserved confounding. The instrumental variable method provided extremely biased estimates of the dose-response effect under violations of the exclusion restriction (no direct effect of treatment assignment on the outcome), though less severe violations of the exclusion restriction should be investigated.
ContributorsMazza, Gina L (Author) / Grimm, Kevin J. (Thesis advisor) / West, Stephen G. (Thesis advisor) / Mackinnon, David P (Committee member) / Tein, Jenn-Yun (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The primary objective in time series analysis is forecasting. Raw data often exhibits nonstationary behavior: trends, seasonal cycles, and heteroskedasticity. After data is transformed to a weakly stationary process, autoregressive moving average (ARMA) models may capture the remaining temporal dynamics to improve forecasting. Estimation of ARMA can be performed

The primary objective in time series analysis is forecasting. Raw data often exhibits nonstationary behavior: trends, seasonal cycles, and heteroskedasticity. After data is transformed to a weakly stationary process, autoregressive moving average (ARMA) models may capture the remaining temporal dynamics to improve forecasting. Estimation of ARMA can be performed through regressing current values on previous realizations and proxy innovations. The classic paradigm fails when dynamics are nonlinear; in this case, parametric, regime-switching specifications model changes in level, ARMA dynamics, and volatility, using a finite number of latent states. If the states can be identified using past endogenous or exogenous information, a threshold autoregressive (TAR) or logistic smooth transition autoregressive (LSTAR) model may simplify complex nonlinear associations to conditional weakly stationary processes. For ARMA, TAR, and STAR, order parameters quantify the extent past information is associated with the future. Unfortunately, even if model orders are known a priori, the possibility of over-fitting can lead to sub-optimal forecasting performance. By intentionally overestimating these orders, a linear representation of the full model is exploited and Bayesian regularization can be used to achieve sparsity. Global-local shrinkage priors for AR, MA, and exogenous coefficients are adopted to pull posterior means toward 0 without over-shrinking relevant effects. This dissertation introduces, evaluates, and compares Bayesian techniques that automatically perform model selection and coefficient estimation of ARMA, TAR, and STAR models. Multiple Monte Carlo experiments illustrate the accuracy of these methods in finding the "true" data generating process. Practical applications demonstrate their efficacy in forecasting.
ContributorsGiacomazzo, Mario (Author) / Kamarianakis, Yiannis (Thesis advisor) / Reiser, Mark R. (Committee member) / McCulloch, Robert (Committee member) / Hahn, Richard (Committee member) / Fricks, John (Committee member) / Arizona State University (Publisher)
Created2018
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Description
This dissertation investigates the classification of systemic lupus erythematosus (SLE) in the presence of non-SLE alternatives, while developing novel curve classification methodologies with wide ranging applications. Functional data representations of plasma thermogram measurements and the corresponding derivative curves provide predictors yet to be investigated for SLE identification. Functional

This dissertation investigates the classification of systemic lupus erythematosus (SLE) in the presence of non-SLE alternatives, while developing novel curve classification methodologies with wide ranging applications. Functional data representations of plasma thermogram measurements and the corresponding derivative curves provide predictors yet to be investigated for SLE identification. Functional nonparametric classifiers form a methodological basis, which is used herein to develop a) the family of ESFuNC segment-wise curve classification algorithms and b) per-pixel ensembles based on logistic regression and fused-LASSO. The proposed methods achieve test set accuracy rates as high as 94.3%, while returning information about regions of the temperature domain that are critical for population discrimination. The undertaken analyses suggest that derivate-based information contributes significantly in improved classification performance relative to recently published studies on SLE plasma thermograms.
ContributorsBuscaglia, Robert, Ph.D (Author) / Kamarianakis, Yiannis (Thesis advisor) / Armbruster, Dieter (Committee member) / Lanchier, Nicholas (Committee member) / McCulloch, Robert (Committee member) / Reiser, Mark R. (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Mediation analysis is used to investigate how an independent variable, X, is related to an outcome variable, Y, through a mediator variable, M (MacKinnon, 2008). If X represents a randomized intervention it is difficult to make a cause and effect inference regarding indirect effects without making no unmeasured confounding assumptions

Mediation analysis is used to investigate how an independent variable, X, is related to an outcome variable, Y, through a mediator variable, M (MacKinnon, 2008). If X represents a randomized intervention it is difficult to make a cause and effect inference regarding indirect effects without making no unmeasured confounding assumptions using the potential outcomes framework (Holland, 1988; MacKinnon, 2008; Robins & Greenland, 1992; VanderWeele, 2015), using longitudinal data to determine the temporal order of M and Y (MacKinnon, 2008), or both. The goals of this dissertation were to (1) define all indirect and direct effects in a three-wave longitudinal mediation model using the causal mediation formula (Pearl, 2012), (2) analytically compare traditional estimators (ANCOVA, difference score, and residualized change score) to the potential outcomes-defined indirect effects, and (3) use a Monte Carlo simulation to compare the performance of regression and potential outcomes-based methods for estimating longitudinal indirect effects and apply the methods to an empirical dataset. The results of the causal mediation formula revealed the potential outcomes definitions of indirect effects are equivalent to the product of coefficient estimators in a three-wave longitudinal mediation model with linear and additive relations. It was demonstrated with analytical comparisons that the ANCOVA, difference score, and residualized change score models’ estimates of two time-specific indirect effects differ as a function of the respective mediator-outcome relations at each time point. The traditional model that performed the best in terms of the evaluation criteria in the Monte Carlo study was the ANCOVA model and the potential outcomes model that performed the best in terms of the evaluation criteria was sequential G-estimation. Implications and future directions are discussed.
ContributorsValente, Matthew J (Author) / Mackinnon, David P (Thesis advisor) / West, Stephen G. (Committee member) / Grimm, Keving (Committee member) / Chassin, Laurie (Committee member) / Arizona State University (Publisher)
Created2018
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Description
In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different

In this work, I present a Bayesian inference computational framework for the analysis of widefield microscopy data that addresses three challenges: (1) counting and localizing stationary fluorescent molecules; (2) inferring a spatially-dependent effective fluorescence profile that describes the spatially-varying rate at which fluorescent molecules emit subsequently-detected photons (due to different illumination intensities or different local environments); and (3) inferring the camera gain. My general theoretical framework utilizes the Bayesian nonparametric Gaussian and beta-Bernoulli processes with a Markov chain Monte Carlo sampling scheme, which I further specify and implement for Total Internal Reflection Fluorescence (TIRF) microscopy data, benchmarking the method on synthetic data. These three frameworks are self-contained, and can be used concurrently so that the fluorescence profile and emitter locations are both considered unknown and, under some conditions, learned simultaneously. The framework I present is flexible and may be adapted to accommodate the inference of other parameters, such as emission photophysical kinetics and the trajectories of moving molecules. My TIRF-specific implementation may find use in the study of structures on cell membranes, or in studying local sample properties that affect fluorescent molecule photon emission rates.
ContributorsWallgren, Ross (Author) / Presse, Steve (Thesis advisor) / Armbruster, Hans (Thesis advisor) / McCulloch, Robert (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Bayesian Additive Regression Trees (BART) is a non-parametric Bayesian model

that often outperforms other popular predictive models in terms of out-of-sample error. This thesis studies a modified version of BART called Accelerated Bayesian Additive Regression Trees (XBART). The study consists of simulation and real data experiments comparing XBART to other leading

Bayesian Additive Regression Trees (BART) is a non-parametric Bayesian model

that often outperforms other popular predictive models in terms of out-of-sample error. This thesis studies a modified version of BART called Accelerated Bayesian Additive Regression Trees (XBART). The study consists of simulation and real data experiments comparing XBART to other leading algorithms, including BART. The results show that XBART maintains BART’s predictive power while reducing its computation time. The thesis also describes the development of a Python package implementing XBART.
ContributorsYalov, Saar (Author) / Hahn, P. Richard (Thesis advisor) / McCulloch, Robert (Committee member) / Kao, Ming-Hung (Committee member) / Arizona State University (Publisher)
Created2019
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Description
The comparison of between- versus within-person relations addresses a central issue in psychological research regarding whether group-level relations among variables generalize to individual group members. Between- and within-person effects may differ in magnitude as well as direction, and contextual multilevel models can accommodate this difference. Contextual multilevel models have been

The comparison of between- versus within-person relations addresses a central issue in psychological research regarding whether group-level relations among variables generalize to individual group members. Between- and within-person effects may differ in magnitude as well as direction, and contextual multilevel models can accommodate this difference. Contextual multilevel models have been explicated mostly for cross-sectional data, but they can also be applied to longitudinal data where level-1 effects represent within-person relations and level-2 effects represent between-person relations. With longitudinal data, estimating the contextual effect allows direct evaluation of whether between-person and within-person effects differ. Furthermore, these models, unlike single-level models, permit individual differences by allowing within-person slopes to vary across individuals. This study examined the statistical performance of the contextual model with a random slope for longitudinal within-person fluctuation data.

A Monte Carlo simulation was used to generate data based on the contextual multilevel model, where sample size, effect size, and intraclass correlation (ICC) of the predictor variable were varied. The effects of simulation factors on parameter bias, parameter variability, and standard error accuracy were assessed. Parameter estimates were in general unbiased. Power to detect the slope variance and contextual effect was over 80% for most conditions, except some of the smaller sample size conditions. Type I error rates for the contextual effect were also high for some of the smaller sample size conditions. Conclusions and future directions are discussed.
ContributorsWurpts, Ingrid Carlson (Author) / Mackinnon, David P (Thesis advisor) / West, Stephen G. (Committee member) / Grimm, Kevin J. (Committee member) / Suk, Hye Won (Committee member) / Arizona State University (Publisher)
Created2016