Statistics and Probability Commons^™

A Review Of Software For Analyzing Molecular Sequences, Haema Nilakanta, Kimberly L. Drews, Suzanne Firrell, Mary A. Foulkes, Kathleen A. Jablonski

GW Biostatistics Center

Background Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are available. But for a new researcher, it is difficult to know which package to choose. We present a systematic review of packages for the analysis of molecular sequences used to describe and compare microbial communities. This review gives students and researchers information to help choose the best analytic pipeline for their project. To the best of our knowledge, this is the first review of such software.

Findings …

Wordless Intervention For Epilepsy In Learning Disabilities (Wield): Study Protocol For A Randomized Controlled Feasibility Trial, Marie-Anne Durand, Bob Gates, Georgina Parkes, Asif Zia

Dartmouth Scholarship

Epilepsy is the most common neurological problem that affects people with learning disabilities. The high seizure frequency, resistance to treatments, associated skills deficit and co-morbidities make the management of epilepsy particularly challenging for people with learning disabilities. The Books Beyond Words booklet for epilepsy uses images to help people with learning disabilities manage their condition and improve quality of life. Our aim is to conduct a randomized controlled feasibility trial exploring key methodological, design and acceptability issues, in order to subsequently undertake a large-scale randomized controlled trial of the Books Beyond Words booklet for epilepsy.

Top Of The Order: Modeling The Optimal Locations Of Minor League Baseball Teams, W. Coleman Conley

Undergraduate Economic Review

Over the last twenty-five years, minor league baseball franchises have defined firm mobility. Revisiting the work of Michael C. Davis (2006), I construct a logistic regression model to predict which cities house minor league baseball teams. Six variables are tested for inclusion in the model, including population, income level, the number of major-league professional sports teams in a city, five-year population change, and distance from the closest professional team. Based on the model's predicted probabilities, cities are ranked in order of highest probability of having a team at each of the different levels from Class A to Class AAA.

Constrained Bayesian Estimation Of Inverse Probability Weights For Nonmonotone Missing Data, Baoluo Sun, Eric J. Tchetgen Tchetgen

Harvard University Biostatistics Working Paper Series

No abstract provided.

Testing Gene-Environment Interactions In The Presence Of Measurement Error, Chongzhi Di, Li Hsu, Charles Kooperberg, Alex Reiner, Ross Prentice

UW Biostatistics Working Paper Series

Complex diseases result from an interplay between genetic and environmental risk factors, and it is of great interest to study the gene-environment interaction (GxE) to understand the etiology of complex diseases. Recent developments in genetics field allows one to study GxE systematically. However, one difficulty with GxE arises from the fact that environmental exposures are often measured with error. In this paper, we focus on testing GxE when the environmental exposure E is subject to measurement error. Surprisingly, contrast to the well-established results that the naive test ignoring measurement error is valid in testing the main effects, we find that …

Personalized Evaluation Of Biomarker Value: A Cost-Benefit Perspective, Ying Huang, Eric Laber

UW Biostatistics Working Paper Series

For a patient who is facing a treatment decision, the added value of information provided by a biomarker depends on the individual patient’s expected response to treatment with and without the biomarker, as well as his/her tolerance of disease and treatment harm. However, individualized estimators of the value of a biomarker are lacking. We propose a new graphical tool named the subject-specific expected benefit curve for quantifying the personalized value of a biomarker in aiding a treatment decision. We develop semiparametric estimators for two general settings: i) when biomarker data are available from a randomized trial; and ii) when biomarker …

Identifying Genetic Variants For Heart Rate Variability In The Acetylcholine Pathway, Harriëtte Riese, Loretto M. Muñoz, Catharina A. Hartman, Xiuhua Ding, Shaoyong Su, Albertine J. Oldehinkel, Arie M. Van Roon, Peter J. Van Der Most, Joop Lefrandt, Ron T. Gansevoort, Pim Van Der Harst, Niek Verweij, Carmilla M. M. Licht, Dorret I. Boomsma, Jouke-Jan Hottenga, Gonneke Willemsen, Brenda W. J. H. Penninx, Ilja M. Nolte, Eco J. C. De Geus, Xiaoling Wang, Harold Snieder

Biostatistics Faculty Publications

Heart rate variability is an important risk factor for cardiovascular disease and all-cause mortality. The acetylcholine pathway plays a key role in explaining heart rate variability in humans. We assessed whether 443 genotyped and imputed common genetic variants in eight key genes (CHAT, SLC18A3, SLC5A7, CHRNB4, CHRNA3, CHRNA, CHRM2 and ACHE) of the acetylcholine pathway were associated with variation in an established measure of heart rate variability reflecting parasympathetic control of the heart rhythm, the root mean square of successive differences (RMSSD) of normal RR intervals. The association was studied in a …

Oscillation Of Second-Order Emden–Fowler Neutral Delay Differential Equations, Ravi P. Agarwal, Martin Bohner, Tongxing Li, Chenghui Zhang

Mathematics and Statistics Faculty Research & Creative Works

We establish some new criteria for the oscillation of second-order Emden–Fowler neutral delay differential equations. We study the case of super linear and the case of sublinear equations subject to various conditions. The results obtained show that the presence of a neutral term in a differential equation can cause or destroy oscillatory properties. Several examples are provided to illustrate the relevance of new theorems.

Cross-Design Synthesis For Extending The Applicability Of Trial Evidence When Treatment Effect Is Heterogeneous-I. Methodology, Ravi Varadhan, Carlos Weiss

Johns Hopkins University, Dept. of Biostatistics Working Papers

Randomized controlled trials (RCTs) provide reliable evidence for approval of new treatments, informing clinical practice, and coverage decisions. The participants in RCTs are often not a representative sample of the larger at-risk population. Hence it is argued that the average treatment effect from the trial is not generalizable to the larger at-risk population. An essential premise of this argument is that there is significant heterogeneity in the treatment effect (HTE). We present a new method to extrapolate the treatment effect from a trial to a target group that is inadequately represented in the trial, when HTE is present. Our method …

Cross-Design Synthesis For Extending The Applicability Of Trial Evidence When Treatment Effect Is Heterogeneous. Part Ii. Application And External Validation, Carlos Weiss, Ravi Varadhan

Johns Hopkins University, Dept. of Biostatistics Working Papers

Randomized controlled trials (RCTs) generally provide the most reliable evidence. When participants in RCTs are selected with respect to characteristics that are potential treatment effect modifiers, the average treatment effect from the trials may not be applicable to a specific target population. We present a new method to project the treatment effect from a RCT to a target group that is inadequately represented in the trial when there is heterogeneity in the treatment effect (HTE). The method integrates RCT and observational data through cross-design synthesis. An essential component is to identify HTE and a calibration factor for unmeasured confounding for …

Retained-Components Factor Transformation: Factor Loadings And Factor Score Predictors In The Column Space Of Retained Components, André Beauducel, Frank Spohn

Journal of Modern Applied Statistical Methods

Factor loadings optimally account for the non-diagonal elements of the covariance matrix of observed variables. Principal component analysis leads to components accounting for a maximum of the variance of the observed variables. Retained-components factor transformation is proposed in order to combine the advantages of factor analysis and principal component analysis.

Pairwise Comparison In Repeated Measures, I.C.A. Oyeka, C. C. Nnanatu

Journal of Modern Applied Statistical Methods

Sometimes a random sample of subjects or patients may be exposed to a battery of diagnostic tests or medication over time and interest is on determining whether there is progressive remission of condition, disease or symptom. Also perhaps early in a program or experiment, subjects or candidates may be required to significantly improve in their performance rates at the current trial relative to an immediately preceding trial, otherwise they may have to withdraw from or drop out. The research interest would then be to determine some critical minimum marginal success rate to guide the management in decision making as well …

A Comparison Of Methods For Group Prediction With High Dimensional Data, Holmes Finch

Journal of Modern Applied Statistical Methods

High dimensional data is the situation in which the number of variables included in an analysis approaches or exceeds the sample size. In the context of group classification, researchers are typically interested in finding a model that can be used to correctly place an individual into their appropriate group; e.g. correctly diagnose individuals with depression. However, when the size of the training sample is small and the number of predictors used to differentiate the groups is larger, standard approaches such as discriminant analysis may not work well. In order to address this issue, statisticians have developed a number of tools …

Objective Priors For Estimation Of Extended Exponential Geometric Distribution, Pedro L. Ramos, Fernando A. Moala, Jorge A. Achcar

Journal of Modern Applied Statistical Methods

A Bayesian analysis was developed with different noninformative prior distributions such as Jeffreys, Maximal Data Information, and Reference. The aim was to investigate the effects of each prior distribution on the posterior estimates of the parameters of the extended exponential geometric distribution, based on simulated data and a real application.

Some General Guidelines For Choosing Missing Data Handling Methods In Educational Research, Jehanzeb R. Cheema

Journal of Modern Applied Statistical Methods

The effect of a number of factors, such as the choice of analytical method, the handling method for missing data, sample size, and proportion of missing data, were examined to evaluate the effect of missing data treatment on accuracy of estimation. A methodological approach involving simulated data was adopted. One outcome of the statistical analyses undertaken in this study is the formulation of easy-to-implement guidelines for educational researchers that allows one to choose one of the following factors when all others are given: sample size, proportion of missing data in the sample, method of analysis, and missing data handling method.

Bayesian Inference For Volatility Of Stock Prices, Juliet G. D'Cunha, K. A. Rao

Journal of Modern Applied Statistical Methods

Lognormal distribution is widely used in the analysis of failure time data and stock prices. Maximum likelihood and Bayes estimator of the coefficient of variation of lognormal distribution along with confidence/credible intervals are developed. The utility of Bayes procedure is illustrated by analyzing prices of selected stocks.

Local Bandwidths For Improving Performance Statistics Of Model-Robust Regression 2, Efosa Edionwe, Julian L. Mbegbu

Journal of Modern Applied Statistical Methods

Model-Robust Regression 2 (MRR2) method is a semi-parametric regression approach that combines parametric and nonparametric fits. The bandwidth controls the smoothness of the nonparametric portion. We present a methodology for deriving data-driven local bandwidth that enhances the performance of MRR2 method for fitting curves to data generated from designed experiments.

Contrast Of Bayesian And Classical Sample Size Determination, Farhana Sadia, Syed S. Hossain

Journal of Modern Applied Statistical Methods

Sample size determination is a prerequisite for statistical surveys. A comprehensive overview of the Bayesian approach for computation of the sample size, and a comparison with classical approaches, is presented. Two surveys are taken as example to illustrate the accuracy and efficiency of each approach, and to make recommendations about which method is preferred. The Bayesian approach of sample size determination may require fewer subjects if proper prior information is available.

The Information Criterion, Masume Ghahramani

Journal of Modern Applied Statistical Methods

The Akaike information criterion, AIC, is widely used for model selection. Using the AIC as the estimator of asymptotic unbias for the second term Kullbake-Leibler risk considers the divergence between the true model and offered models. However, it is an inconsistent estimator. A proposed approach the problem is the use of A'IC, a consistently offered information criterion. Model selection of classic and linear models are considered by a Monte Carlo simulation.

Gumbel-Weibull Distribution: Properties And Applications, Raid Al-Aqtash, Carl Lee, Felix Famoye

Journal of Modern Applied Statistical Methods

Some properties of the Gumbel-Weibull distribution including the mean deviations and modes are studied. A detailed discussion of regions of unimodality and bimodality is given. The method of maximum likelihood is proposed for estimating the distribution parameters and a simulation is conducted to study the performance of the method. Three tests are given for testing the significance of a distribution parameter. The applications of Gumbel-Weibull distribution are emphasized. Five data sets are used to illustrate the flexibility of the distribution in fitting unimodal and bimodal data sets.

Fitting Stereotype Logistic Regression Models For Ordinal Response Variables In Educational Research (Stata), Xing Liu

Journal of Modern Applied Statistical Methods

The stereotype logistic (SL) model is an alternative to the proportional odds (PO) model for ordinal response variables when the proportional odds assumption is violated. This model seems to be underutilized. One major reason is the constraint of current statistical software packages. Statistical Package for the Social Sciences (SPSS) cannot perform the SL regression analysis, and SAS does not have the procedure developed to directly estimate the model. The purpose of this article was to illustrate the stereotype logistic (SL) regression model, and apply it to estimate mathematics proficiency level of high school students using Stata. In addition, it compared …

Optimal Location Design For Prediction Of Spatial Correlated Environmental Functional Data, Mahdi Rasekhi, B. Jamshidi, F. Rivaz

Journal of Modern Applied Statistical Methods

The optimal choice of sites to make spatial prediction is critical for a better understanding of really spatio-temporal data. It is important to obtain the essential spatio-temporal variability of the process in determining optimal design, because these data tend to exhibit both spatial and temporal variability. Two new methods of prediction for spatially correlated functional data are considered. The first method models spatial dependency by fitting variogram to empirical variogram, similar to ordinary kriging (univariate approach). The second method models spatial dependency by linear model co-regionalization (multivariate approach). The variance of prediction method was chosen as the optimization design criterion. …

Missing Data And The Statistical Modeling Of Adolescent Pregnancy, Dudley L. Poston Dr., Eugenia Conde Dr.

Journal of Modern Applied Statistical Methods

Missing data is a pervasive problem in social science research. Many techniques have been developed to handle the problem. Different ways of handling missing data were shown to lead to different results in statistical models. A demonstration was given based on statistical modeling of the likelihood of a woman reporting having had an adolescent pregnancy by handling missing data with several different approaches. Results indicate that many of the independent variables in the model vary in whether they are, or are not, statistically significant in predicting the log odds of a woman having a teen pregnancy, and in the ranking …

Conover’S F Test As An Alternative To Durbin’S Test, Donald J. Best, John Charles Rayner

Journal of Modern Applied Statistical Methods

Data consisting of ranks within blocks are considered for balanced incomplete block designs. An F test statistic from ANOVA is better approximated by an F distribution than the Durbin statistic is approximated by a chi-squared distribution. Indicative powers demonstrate that the F test is generally superior to Durbin’s test.

A Bivariate Distribution With Conditional Gamma And Its Multivariate Form, Sumen Sen, Rajan Lamichhane, Norou Diawara

Journal of Modern Applied Statistical Methods

A bivariate distribution whose marginal are gamma and beta prime distribution is introduced. The distribution is derived and the generation of such bivariate sample is shown. Extension of the results are given in the multivariate case under a joint independent component analysis method. Simulated applications are given and they show consistency of our approach. Estimation procedures for the bivariate case are provided.

Reliability Estimates Of Generalized Poisson Distribution And Generalized Geometric Series Distribution, Adil H. Khan, T R. Jan

Journal of Modern Applied Statistical Methods

Discrete distributions have played an important role in the reliability theory. In order to obtain Bayes estimators, researchers have adopted various conventional techniques. Generalizing the results of Maiti (1995), Chaturvadi and Tomer (2002) dealt with the problem of estimating P{X₁, X₂, …, X_k ≤ Y}, where random variables X and Y were assumed to follow a negative binomial distribution. Agit et al. obtained Bayesian estimates of the reliability functions and P{X₁, X₂, …, X_k ≤ Y} considering X and Y following binomial and Poisson …

Comparison Of Individual And Moving Range Chart Combinations To Individual Charts In Terms Of Arl After Designing For A Common “All Ok” Arl, Dewi Rahardja

Journal of Modern Applied Statistical Methods

In some process monitoring situations, consecutive measurements are spaced widely apart in time, making monitoring process aim and spread difficult. This study uses three cases to compare the effectiveness of two such monitoring schemes, i.e., the X chart alone (X-only chart) and the Individuals and Moving Range Chart Combination (X/MR chars), in terms of Average Run Length (ARL) after designing for a common “all OK” (in-control) ARL. The study finds that X chart alone is sufficient (and hence, recommended) in detecting changes in all the 3 cases: changes in the process mean, changes in the process standard deviation, and changes …

Front Matter, Jmasm Editors

Journal of Modern Applied Statistical Methods

.

Improved Randomization Tests For A Class Of Single-Case Intervention Designs, Joel R. Levin, John M. Ferron, Boris S. Gafurov

Journal of Modern Applied Statistical Methods

Forty years ago, Eugene Edgington developed a single-case AB intervention design-and-analysis procedure based on a random determination of the point at which the B phase would start. In the present simulation studies encompassing a variety of AB-type contexts, it is demonstrated that by also randomizing the order in which the A and B phases are administered, a researcher can markedly increase the procedure’s statistical power.

Robust Winsorized Shrinkage Estimators For Linear Regression Model, Nileshkumar H. Jadhav, D N. Kashid

Journal of Modern Applied Statistical Methods

In multiple linear regression, the ordinary least squares estimator is very sensitive to the presence of multicollinearity and outliers in the response variable. To handle these problems in the data, Winsorized shrinkage estimators are proposed and the performance of these estimators is evaluated through mean square error sense.