Statistical Models Commons^™

Stability Of Single-Parent Gene Expression Complementation In Maize Hybrids Upon Water Deficit Stress, Caroline Marcon, Anja Paschold, Waqas Ahmed Malik, Andrew Lithio, Jutta A. Baldauf, Lena Altrogge, Nina Opitz, Christa Lanz, Heiko Schoof, Dan Nettleton, Hans-Peter Piepho, Frank Hochholdinger

Dan Nettleton

Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment. Single-parent expression (SPE) of genes is an extreme instance of gene expression complementation, in which genes are active in only one of two parents but are expressed in both reciprocal hybrids. In this study, 1,997 genes only expressed in B73 and 2,024 genes …

Genomic Neighborhoods For Arabidopsisretrotransposons: A Role For Targeted Integration In The Distribution Of The Metaviridae, Brooke D. Peterson-Burch, Dan Nettleton, Daniel F. Voytas

Dan Nettleton

Background: Retrotransposons are an abundant component of eukaryotic genomes. The high quality of the Arabidopsis thaliana genome sequence makes it possible to comprehensively characterize retroelement populations and explore factors that contribute to their genomic distribution.

Results: We identified the full complement of A. thaliana long terminal repeat (LTR) retroelements using RetroMap, a software tool that iteratively searches genome sequences for reverse transcriptases and then defines retroelement insertions. Relative ages of full-length elements were estimated by assessing sequence divergence between LTRs: the Pseudoviridae were significantly younger than the Metaviridae. All retroelement insertions were mapped onto the genome sequence and their distribution …

Empirical Bayes Analysis Of Rna-Seq Data For Detection Of Gene Expression Heterosis, Jarad Niemi, Eric Mittman, Will Landau, Dan Nettleton

Dan Nettleton

An important type of heterosis, known as hybrid vigor, refers to the enhancements in the phenotype of hybrid progeny relative to their inbred parents. Although hybrid vigor is extensively utilized in agriculture, its molecular basis is still largely unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers are measuring transcript abundance levels of thousands of genes in parental inbred lines and their hybrid offspring using RNA sequencing (RNA-seq) technology. The resulting data allow researchers to search for evidence of gene expression heterosis as one potential molecular mechanism underlying heterosis of agriculturally important traits. The null hypotheses …

Penalized Nonparametric Scalar-On-Function Regression Via Principal Coordinates, Philip T. Reiss, David L. Miller, Pei-Shien Wu, Wen-Yu Hua

Philip T. Reiss

Depicting Estimates Using The Intercept In Meta-Regression Models: The Moving Constant Technique, Blair T. Johnson Dr., Tania B. Huedo-Medina Dr.

Blair T. Johnson

In any scientific discipline, the ability to portray research patterns graphically often aids greatly in interpreting a phenomenon. In part to depict phenomena, the statistics and capabilities of meta-analytic models have grown increasingly sophisticated. Accordingly, this article details how to move the constant in weighted meta-analysis regression models (viz. “meta-regression”) to illuminate the patterns in such models across a range of complexities. Although it is commonly ignored in practice, the constant (or intercept) in such models can be indispensible when it is not relegated to its usual static role. The moving constant technique makes possible estimates and confidence intervals at …

A Comparative Analysis Of Decision Trees Vis-À-Vis Other Computational Data Mining Techniques In Automotive Insurance Fraud Detection, Adrian Gepp, Kuldeep Kumar, J Holton Wilson, Sukanto Bhattacharya

Kuldeep Kumar

No abstract provided.

A General Framework For Infrastructure System Reliability Modelling And Analysis, Payam Mokhtarian, Mohammad-Reza Namazi-Rad, Tin Kin Ho, Mahmoud Efatmaneshnik

Payam Mokhtarian

An infrastructure system is inherently complex, with layers of both explicitly defined and hidden or subtle interfaces with other infrastructure systems and human users. High availability is desired, which implies stringent requirements on reliability and safety. Reliability analysis typically starts at component or sub-system level and aggregates through the system functional hierarchy. Because of the system complexity, incorporating occurrences of all possible interactions and scenarios is not always practical and failure data is often limited. Moreover, there are unobserved events among the sub-systems distributing either randomly or with temporal trend. To facilitate reliability analysis amid the complex environment and uncertain …

A Probabilistic Predictive Model For Residential Mobility In Australia, Mohammad-Reza Namazi-Rad, Nagesh Shukla, Albert Munoz, Payam Mokhtarian, Jun Ma

Payam Mokhtarian

Household relocation modelling is an integral part of the planning process as residential movements influence the demand for community facilities and services. Department of Families, Housing, Community Services and Indigenous Affairs (FaHCSIA) created the Household, Income and Labour Dynamics in Australia (HILDA) program to collect reliable longitudinal data on family and household dynamics. Socio-demographic information (such as general health situation and well-being, lifestyle changes, residential mobility, income and welfare dynamics, and labour market dynamics) is collected from the sampled individuals and households. The data shows that approximately 17% of Australian households and 13% of couple families in the HILDA sample …

From Amazon To Apple: Modeling Online Retail Sales, Purchase Incidence And Visit Behavior, Anastasios Panagiotelis, Michael S. Smith, Peter Danaher

Michael Stanley Smith

In this study we propose a multivariate stochastic model for website visit duration, page views, purchase incidence and the sale amount for online retailers. The model is constructed by composition from carefully selected distributions, and involves copula components. It allows for the strong nonlinear relationships between the sales and visit variables to be explored in detail, and can be used to construct sales predictions. The model is readily estimated using maximum likelihood, making it an attractive choice in practice given the large sample sizes that are commonplace in online retail studies. We examine a number of top-ranked U.S. online retailers, …

Spectral Density Shrinkage For High-Dimensional Time Series, Mark Fiecas, Rainer Von Sachs

Mark Fiecas

Hierarchical Vector Auto-Regressive Models And Their Applications To Multi-Subject Effective Connectivity, Cristina Gorrostieta, Mark Fiecas, Hernando Ombao, Erin Burke, Steven Cramer

Mark Fiecas

A Comparison Of Periodic Autoregressive And Dynamic Factor Models In Intraday Energy Demand Forecasting, Thomas Mestekemper, Goeran Kauermann, Michael Smith

Michael Stanley Smith

We suggest a new approach for forecasting energy demand at an intraday resolution. Demand in each intraday period is modeled using semiparametric regression smoothing to account for calendar and weather components. Residual serial dependence is captured by one of two multivariate stationary time series models, with dimension equal to the number of intraday periods. These are a periodic autoregression and a dynamic factor model. We show the benefits of our approach in the forecasting of district heating demand in a steam network in Germany and aggregate electricity demand in the state of Victoria, Australia. In both studies, accounting for weather …

Bayesian Approaches To Copula Modelling, Michael S. Smith

Michael Stanley Smith

Copula models have become one of the most widely used tools in the applied modelling of multivariate data. Similarly, Bayesian methods are increasingly used to obtain efficient likelihood-based inference. However, to date, there has been only limited use of Bayesian approaches in the formulation and estimation of copula models. This article aims to address this shortcoming in two ways. First, to introduce copula models and aspects of copula theory that are especially relevant for a Bayesian analysis. Second, to outline Bayesian approaches to formulating and estimating copula models, and their advantages over alternative methods. Copulas covered include Archimedean, copulas constructed …

Time Series, Unit Roots, And Cointegration: An Introduction, Lonnie K. Stevans

Lonnie K. Stevans

The econometric literature on unit roots took off after the publication of the paper by Nelson and Plosser (1982) that argued that most macroeconomic series have unit roots and that this is important for the analysis of macroeconomic policy. Yule (1926) suggested that regressions based on trending time series data can be spurious. This problem of spurious correlation was further pursued by Granger and Newbold (1974) and this also led to the development of the concept of cointegration (lack of cointegration implies spurious regression). The pathbreaking paper by Granger (1981), first presented at a conference at the University of Florida …

Big Data And The Future, Sherri Rose

Sherri Rose

No abstract provided.

A Comparative Analysis Of Decision Trees Vis-À-Vis Other Computational Data Mining Techniques In Automotive Insurance Fraud Detection, Adrian Gepp, Kuldeep Kumar, J Holton Wilson, Sukanto Bhattacharya

Adrian Gepp

No abstract provided.

Modeling Dependence Using Skew T Copulas: Bayesian Inference And Applications, Michael S. Smith, Quan Gan, Robert Kohn

Michael Stanley Smith

[THIS IS AN AUGUST 2010 REVISION THAT REPLACES ALL PREVIOUS VERSIONS.]

We construct a copula from the skew t distribution of Sahu, Dey & Branco (2003). This copula can capture asymmetric and extreme dependence between variables, and is one of the few copulas that can do so and still be used in high dimensions effectively. However, it is difficult to estimate the copula model by maximum likelihood when the multivariate dimension is high, or when some or all of the marginal distributions are discrete-valued, or when the parameters in the marginal distributions and copula are estimated jointly. We therefore propose …

Estimation Of Copula Models With Discrete Margins Via Bayesian Data Augmentation, Michael S. Smith, Mohamad A. Khaled

Michael Stanley Smith

Estimation of copula models with discrete margins is known to be difficult beyond the bivariate case. We show how this can be achieved by augmenting the likelihood with latent variables, and computing inference using the resulting augmented posterior. To evaluate this we propose two efficient Markov chain Monte Carlo sampling schemes. One generates the latent variables as a block using a Metropolis-Hasting step with a proposal that is close to its target distribution, the other generates them one at a time. Our method applies to all parametric copulas where the conditional copula functions can be evaluated, not just elliptical copulas …

Rejoinder: Estimation Issues For Copulas Applied To Marketing Data, Peter Danaher, Michael Smith

Michael Stanley Smith

Estimating copula models using Bayesian methods presents some subtle challenges, ranging from specification of the prior to computational tractability. There is also some debate about what is the most appropriate copula to employ from those available. We address these issues here and conclude by discussing further applications of copula models in marketing.

Forecasting Television Ratings, Peter Danaher, Tracey Dagger, Michael Smith

Michael Stanley Smith

Despite the state of flux in media today, television remains the dominant player globally for advertising spend. Since television advertising time is purchased on the basis of projected future ratings, and ad costs have skyrocketed, there is increasing pressure to forecast television ratings accurately. Previous forecasting methods are not generally very reliable and many have not been validated, but more distressingly, none have been tested in today’s multichannel environment. In this study we compare 8 different forecasting models, ranging from a naïve empirical method to a state-of-the-art Bayesian model-averaging method. Our data come from a recent time period, 2004-2008 in …

Windows Executable For Gaussian Copula With Nbd Margins, Michael S. Smith

Michael Stanley Smith

This is an example Windows 32bit program to estimate a Gaussian copula model with NBD margins. The margins are estimated first using MLE, and the copula second using Bayesian MCMC. The model was discussed in Danaher & Smith (2011; Marketing Science) as example 4 (section 4.2).

Modeling Multivariate Distributions Using Copulas: Applications In Marketing, Peter J. Danaher, Michael S. Smith

Michael Stanley Smith

In this research we introduce a new class of multivariate probability models to the marketing literature. Known as “copula models”, they have a number of attractive features. First, they permit the combination of any univariate marginal distributions that need not come from the same distributional family. Second, a particular class of copula models, called “elliptical copula”, have the property that they increase in complexity at a much slower rate than existing multivariate probability models as the number of dimensions increase. Third, they are very general, encompassing a number of existing multivariate models, and provide a framework for generating many more. …

Bicycle Commuting In Melbourne During The 2000s Energy Crisis: A Semiparametric Analysis Of Intraday Volumes, Michael S. Smith, Goeran Kauermann

Michael Stanley Smith

Cycling is attracting renewed attention as a mode of transport in western urban environments, yet the determinants of usage are poorly understood. In this paper we investigate some of these using intraday bicycle volumes collected via induction loops located at ten bike paths in the city of Melbourne, Australia, between December 2005 and June 2008. The data are hourly counts at each location, with temporal and spatial disaggregation allowing for the impact of meteorology to be measured accurately for the first time. Moreover, during this period petrol prices varied dramatically and the data also provide a unique opportunity to assess …

The Generalized Shrinkage Estimator For The Analysis Of Functional Connectivity Of Brain Signals, Mark Fiecas, Hernando Ombao

Mark Fiecas

We develop a new statistical method for estimating functional connectivity between neurophysiological signals represented by a multivariate time series. We use partial coherence as the measure of functional connectivity. Partial coherence identifies the frequency bands that drive the direct linear association between any pair of channels. To estimate partial coherence, one would first need an estimate of the spectral density matrix of the multivariate time series. Parametric estimators of the spectral density matrix provide good frequency resolution but could be sensitive when the parametric model is misspecified. Smoothing-based nonparametric estimators are robust to model misspecification and are consistent but may …

An Introduction To Propensity-Score Methods For Reducing Confounding In Observational Studies, Peter C. Austin

Peter Austin

The propensity score is the probability of treatment assignment conditional on observed baseline characteristics. The propensity score allows one to design and analyze an observational (non-randomized) study so that it mimics some of the particular characteristics of a randomized controlled trial. In particular, the propensity score is a balancing score: conditional on the propensity score, the distribution of observed baseline covariates will be similar between treated and untreated subjects. We describe four different propensity score methods: matching on the propensity score, stratification on the propensity score, inverse probability of treatment weighting using the propensity score, and covariate adjustment using the …

Modeling Longitudinal Data Using A Pair-Copula Decomposition Of Serial Dependence, Michael S. Smith, Aleksey Min, Carlos Almeida, Claudia Czado

Michael Stanley Smith

Copulas have proven to be very successful tools for the flexible modelling of cross-sectional dependence. In this paper we express the dependence structure of continuous-valued time series data using a sequence of bivariate copulas. This corresponds to a type of decomposition recently called a ‘vine’ in the graphical models literature, where each copula is entitled a ‘pair-copula’. We propose a Bayesian approach for the estimation of this dependence structure for longitudinal data. Bayesian selection ideas are used to identify any independence pair-copulas, with the end result being a parsimonious representation of a time-inhomogeneous Markov process of varying order. Estimates are …

Men In Black: The Impact Of New Contracts On Football Referees’ Performances, Babatunde Buraimo, Alex Bryson, Rob Simmons

Dr Babatunde Buraimo

No abstract provided.

The 1905 Einstein Equation In A General Mathematical Analysis Model Of Quasars, Byron E. Bell

Byron E. Bell

Fast Function-On-Scalar Regression With Penalized Basis Expansions, Philip T. Reiss, Lei Huang, Maarten Mennes

Lei Huang

Regression models for functional responses and scalar predictors are often fitted by means of basis functions, with quadratic roughness penalties applied to avoid overfitting. The fitting approach described by Ramsay and Silverman in the 1990s amounts to a penalized ordinary least squares (P-OLS) estimator of the coefficient functions. We recast this estimator as a generalized ridge regression estimator, and present a penalized generalized least squares (P-GLS) alternative. We describe algorithms by which both estimators can be implemented, with automatic selection of optimal smoothing parameters, in a more computationally efficient manner than has heretofore been available. We discuss pointwise confidence intervals …

The 1905 Einstein Equation In A General Mathematical Analysis Model Of Quasars, Byron E. Bell

Byron E. Bell

No abstract provided.