Stan is a probabilistic programming language for specifying statistical models. A Stan program imperatively defines a log probability function over parameters conditioned on specified data and constants. As of version 2.14.0, Stan provides full Bayesian inference for continuous-variable models through Markov chain Monte Carlo methods such as the…

The uncertainty arising from item parameter estimation is often not negligible and must be accounted for when calculating latent variable (LV) scores in item response theory (IRT). It is particularly so when the calibration sample size is limited and/or the calibration IRT model is complex. In the current work, we treat two-stage IRT scoring as a…

Inferring causal effects of treatments is a central goal in many disciplines. The potential outcomes framework is a main statistical approach to causal inference, in which a causal effect is defined as a comparison of the potential outcomes of the same units under different treatment conditions. Because for each unit at most one of the potential…

Although immediacy is one of the necessary criteria to show strong evidence of a causal relation in SCDs, no inferential statistical tool is currently used to demonstrate it. We propose a Bayesian unknown change-point model to investigate and quantify immediacy in SCD analysis. Unlike visual analysis that considers only 3-5 observations in…

This paper attempts to bridge the gap between classical test theory and item response theory. It is demonstrated that the familiar and popular statistics used in classical test theory can be translated into a Bayesian framework where all of the advantages of the Bayesian paradigm can be realized. In particular, prior opinion can be introduced and…

Null hypothesis significance testing (NHST) has been the subject of debate for decades and alternative approaches to data analysis have been proposed. This article addresses this debate from the perspective of scientific inquiry and inference. Inference is an inverse problem and application of statistical methods cannot reveal whether effects…

Convergent research suggests that people with ASD have difficulties localizing sounds in space. These difficulties have implications for communication, the development of social behavior, and quality of life. Recently, a theory has emerged which treats perceptual symptoms in ASD as the product of impairments in implicit Bayesian inference; as…

Bayesian statistical methods have become more feasible to implement with advances in computing but are not commonly used in educational research. In contrast to frequentist approaches that take hypotheses (and the associated parameters) as fixed, Bayesian methods take data as fixed and hypotheses as random. This difference means that Bayesian…

A review of the software Just Another Gibbs Sampler (JAGS) is provided. We cover aspects related to history and development and the elements a user needs to know to get started with the program, including (a) definition of the data, (b) definition of the model, (c) compilation of the model, and (d) initialization of the model. An example using a…

When estimating causal effects, unmeasured confounding and model misspecification are both potential sources of bias. We propose a method to simultaneously address both issues in the form of a semi-parametric sensitivity analysis. In particular, our approach incorporates Bayesian Additive Regression Trees into a two-parameter sensitivity analysis…

When fitting hierarchical regression models, maximum likelihood (ML) estimation has computational (and, for some users, philosophical) advantages compared to full Bayesian inference, but when the number of groups is small, estimates of the covariance matrix (S) of group-level varying coefficients are often degenerate. One can do better, even from…

When fitting hierarchical regression models, maximum likelihood (ML) estimation has computational (and, for some users, philosophical) advantages compared to full Bayesian inference, but when the number of groups is small, estimates of the covariance matrix [sigma] of group-level varying coefficients are often degenerate. One can do better, even…

We extend a unified and easy-to-use approach to measurement error and missing data. In our companion article, Blackwell, Honaker, and King give an intuitive overview of the new technique, along with practical suggestions and empirical applications. Here, we offer more precise technical details, more sophisticated measurement error model…

The purpose of this paper is to provide an easy template for the inclusion of the Bayes factor in reporting experimental results, particularly as a recommendation for articles in the "Journal of Problem Solving." The Bayes factor provides information with a similar purpose to the "p"-value--to allow the researcher to make…

The main goal of this research is to design, implement, and evaluate a novel explanation method, the hierarchical explanation method (HEM), for explaining Bayesian network (BN) inference when the network is modeling a population of conditionally independent agents, each of which is modeled as a subnetwork. For example, consider disease-outbreak…