Bayesian Analysis of Nonlinear Structural Equation Models with Nonignorable Missing Data

A Bayesian approach is developed for analyzing nonlinear structural equation models with nonignorable missing data. The nonignorable missingness mechanism is specified by a logistic regression model. A hybrid algorithm that combines the Gibbs sampler and the Metropolis–Hastings algorithm is used to produce the joint Bayesian estimates of structural parameters, latent variables, parameters in the nonignorable missing model, as well as their standard errors estimates. A goodness-of-fit statistic for assessing the plausibility of the posited nonlinear structural equation model is introduced, and a procedure for computing the Bayes factor for model comparison is developed via path sampling. Results obtained with respect to different missing data models, and different prior inputs are compared via simulation studies. In particular, it is shown that in the presence of nonignorable missing data, results obtained by the proposed method with a nonignorable missing data model are significantly better than those that are obtained under the missing at random assumption. A real example is presented to illustrate the newly developed Bayesian methodologies. This research is fully supported by a grant (CUHK 4243/03H) from the Research Grant Council of the Hong Kong Special Administration Region. The authors are thankful to the editor and reviewers for valuable comments for improving the paper, and also to ICPSR and the relevant funding agency for allowing the use of the data. Requests for reprints should be sent to Professor S.Y. Lee, Department of Statistics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.     

Bayesian analysis of mixtures in structural equation models with non‐ignorable missing data

Structural equation models (SEMs) have become widely used to determine the interrelationships between latent and observed variables in social, psychological, and behavioural sciences. As heterogeneous data are very common in practical research in these fields, the analysis of mixture models has received a lot of attention in the literature. An important issue in the analysis of mixture SEMs is the presence of missing data, in particular of data missing with a non‐ignorable mechanism. However, only a limited amount of work has been done in analysing mixture SEMs with non‐ignorable missing data. The main objective of this paper is to develop a Bayesian approach for analysing mixture SEMs with an unknown number of components and non‐ignorable missing data. A simulation study shows that Bayesian estimates obtained by the proposed Markov chain Monte Carlo methods are accurate and the Bayes factor computed via a path sampling procedure is useful for identifying the correct number of components, selecting an appropriate missingness mechanism, and investigating various effects of latent variables in the mixture SEMs. A real data set on a study of job satisfaction is used to demonstrate the methodology.     

Analysis of structural equation model with ignorable missing continuous and polytomous data

The main purpose of this article is to develop a Bayesian approach for structural equation models with ignorable missing continuous and polytomous data. Joint Bayesian estimates of thresholds, structural parameters and latent factor scores are obtained simultaneously. The idea of data augmentation is used to solve the computational difficulties involved. In the posterior analysis, in addition to the real missing data, latent variables and latent continuous measurements underlying the polytomous data are treated as hypothetical missing data. An algorithm that embeds the Metropolis-Hastings algorithm within the Gibbs sampler is implemented to produce the Bayesian estimates. A goodness-of-fit statistic for testing the posited model is presented. It is shown that the proposed approach is not sensitive to prior distributions and can handle situations with a large number of missing patterns whose underlying sample sizes may be small. Computational efficiency of the proposed procedure is illustrated by simulation studies and a real example.The work described in this paper was fully supported by a grant from the Research Grants Council of the HKSAR (Project No. CUHK 4088/99H). The authors are greatly indebted to the Editor and anonymous reviewers for valuable comments in improving the paper; and also to D. E. Morisky and J.A. Stein for the use of their AIDS data set.     

2PL模型的两种马尔可夫蒙特卡洛缺失数据处理方法比较

马尔科夫蒙特卡洛（MCMC）是项目反应理论中处理缺失数据的一种典型方法。文章通过模拟研究比较了在不同被试人数,项目数,缺失比例下两种MCMC方法（M-H within Gibbs和DA-T Gibbs）参数估计的精确性,并结合了实证研究。研究结果表明,两种方法是有差异的,项目参数估计均受被试人数影响很大,受缺失比例影响相对更小。在样本较大缺失比例较小时,M-H within Gibbs参数估计的均方误差（RMSE）相对略小,随着样本数的减少或缺失比例的增加,DA-T Gibbs方法逐渐优于M-H within Gibbs方法     

Model comparison of nonlinear structural equation models with fixed covariates

Recently, it has been recognized that the commonly used linear structural equation model is inadequate to deal with some complicated substantive theory. A new nonlinear structural equation model with fixed covariates is proposed in this article. A procedure, which utilizes the powerful path sampling for computing the Bayes factor, is developed for model comparison. In the implementation, the required random observations are simulated via a hybrid algorithm that combines the Gibbs sampler and the Metropolis-Hastings algorithm. It is shown that the proposed procedure is efficient and flexible; and it produces Bayesian estimates of the parameters, latent variables, and their highest posterior density intervals as by-products. Empirical performances of the proposed procedure such as sensitivity to prior inputs are illustrated by a simulation study and a real example.This research is fully supported by a grant from the Research Grant Council of the Hong Kong Special Administrative Region, China (Project No. CUHK 4346/01H). The authors are thankful to the Editor, the Associate Editor, and anonymous reviewers for valuable comments which improve the paper significantly, and grateful to ICPSR and the relevant funding agency for allowing use of the data in the example. The assistance of Michael K.H. Leung and Esther L.S. Tam is gratefully acknowledged.     

A bayesian approach to confirmatory factor analysis

Confirmatory factor analysis is considered from a Bayesian viewpoint, in which prior information on parameter is incorporated in the analysis. An iterative algorithm is developed to obtain the Bayes estimates. A numerical example based on longitudinal data is presented. A simulation study is designed to compare the Bayesian approach with the maximum likelihood method.Computer facilities were provided by the Computer Services Center, The Chinese University of Hong Kong.     

Bayesian model selection for mixtures of structural equation models with an unknown number of components

This paper considers mixtures of structural equation models with an unknown number of components. A Bayesian model selection approach is developed based on the Bayes factor. A procedure for computing the Bayes factor is developed via path sampling, which has a number of nice features. The key idea is to construct a continuous path linking the competing models; then the Bayes factor can be estimated efficiently via grids in [0, 1] and simulated observations that are generated by the Gibbs sampler from the posterior distribution. Bayesian estimates of the structural parameters, latent variables, as well as other statistics can be produced as by‐products. The properties and merits of the proposed procedure are discussed and illustrated by means of a simulation study and a real example.     

Bayes factors for testing inequality constrained hypotheses: Issues with prior specification

Several issues are discussed when testing inequality constrained hypotheses using a Bayesian approach. First, the complexity (or size) of the inequality constrained parameter spaces can be ignored. This is the case when using the posterior probability that the inequality constraints of a hypothesis hold, Bayes factors based on non‐informative improper priors, and partial Bayes factors based on posterior priors. Second, the Bayes factor may not be invariant for linear one‐to‐one transformations of the data. This can be observed when using balanced priors which are centred on the boundary of the constrained parameter space with a diagonal covariance structure. Third, the information paradox can be observed. When testing inequality constrained hypotheses, the information paradox occurs when the Bayes factor of an inequality constrained hypothesis against its complement converges to a constant as the evidence for the first hypothesis accumulates while keeping the sample size fixed. This paradox occurs when using Zellner's g prior as a result of too much prior shrinkage. Therefore, two new methods are proposed that avoid these issues. First, partial Bayes factors are proposed based on transformed minimal training samples. These training samples result in posterior priors that are centred on the boundary of the constrained parameter space with the same covariance structure as in the sample. Second, a g prior approach is proposed by letting g go to infinity. This is possible because the Jeffreys–Lindley paradox is not an issue when testing inequality constrained hypotheses. A simulation study indicated that the Bayes factor based on this g prior approach converges fastest to the true inequality constrained hypothesis.     

A tutorial on Bayes factor estimation with the product space method

The Bayes factor is an intuitive and principled model selection tool from Bayesian statistics. The Bayes factor quantifies the relative likelihood of the observed data under two competing models, and as such, it measures the evidence that the data provides for one model versus the other. Unfortunately, computation of the Bayes factor often requires sampling-based procedures that are not trivial to implement. In this tutorial, we explain and illustrate the use of one such procedure, known as the product space method (Carlin & Chib, 1995). This is a transdimensional Markov chain Monte Carlo method requiring the construction of a “supermodel” encompassing the models under consideration. A model index measures the proportion of times that either model is visited to account for the observed data. This proportion can then be transformed to yield a Bayes factor. We discuss the theory behind the product space method and illustrate, by means of applied examples from psychological research, how the method can be implemented in practice.     

Bayesian analysis of two‐level nonlinear structural equation models with continuous and polytomous data

Two‐level structural equation models with mixed continuous and polytomous data and nonlinear structural equations at both the between‐groups and within‐groups levels are important but difficult to deal with. A Bayesian approach is developed for analysing this kind of model. A Markov chain Monte Carlo procedure based on the Gibbs sampler and the Metropolis‐Hasting algorithm is proposed for producing joint Bayesian estimates of the thresholds, structural parameters and latent variables at both levels. Standard errors and highest posterior density intervals are also computed. A procedure for computing Bayes factor, based on the key idea of path sampling, is established for model comparison.     

Modeling Dependence Structures for Response Times in a Bayesian Framework

A multivariate generalization of the log-normal model for response times is proposed within an innovative Bayesian modeling framework. A novel Bayesian Covariance Structure Model (BCSM) is proposed, where the inclusion of random-effect variables is avoided, while their implied dependencies are modeled directly through an additive covariance structure. This makes it possible to jointly model complex dependencies due to for instance the test format (e.g., testlets, complex constructs), time limits, or features of digitally based assessments. A class of conjugate priors is proposed for the random-effect variance parameters in the BCSM framework. They give support to testing the presence of random effects, reduce boundary effects by allowing non-positive (co)variance parameters, and support accurate estimation even for very small true variance parameters. The conjugate priors under the BCSM lead to efficient posterior computation. Bayes factors and the Bayesian Information Criterion are discussed for the purpose of model selection in the new framework. In two simulation studies, a satisfying performance of the MCMC algorithm and of the Bayes factor is shown. In comparison with parameter expansion through a half-Cauchy prior, estimates of variance parameters close to zero show no bias and undercoverage of credible intervals is avoided. An empirical example showcases the utility of the BCSM for response times to test the influence of item presentation formats on the test performance of students in a Latin square experimental design.

     

Bayesian model selection of informative hypotheses for repeated measurements

When analyzing repeated measurements data, researchers often have expectations about the relations between the measurement means. The expectations can often be formalized using equality and inequality constraints between (i) the measurement means over time, (ii) the measurement means between groups, (iii) the means adjusted for time-invariant covariates, and (iv) the means adjusted for time-varying covariates. The result is a set of informative hypotheses. In this paper, the Bayes factor is used to determine which hypothesis receives most support from the data. A pivotal element in the Bayesian framework is the specification of the prior. To avoid subjective prior specification, training data in combination with restrictions on the measurement means are used to obtain so-called constrained posterior priors. A simulation study and an empirical example from developmental psychology show that this prior results in Bayes factors with desirable properties.     

Bayesian estimation and model selection in ordered latent class models for polytomous items

In a latent class IRT model in which the latent classes are ordered on one dimension, the class specific response probabilities are subject to inequality constraints. The number of these inequality constraints increase dramatically with the number of response categories per item, if assumptions like monotonicity or double monotonicity of the cumulative category response functions are postulated. A Markov chain Monte Carlo method, the Gibbs sampler, can sample from the multivariate posterior distribution of the parameters under the constraints. Bayesian model selection can be done by posterior predictive checks and Bayes factors. A simulation study is done to evaluate results of the application of these methods to ordered latent class models in three realistic situations. Also, an example of the presented methods is given for existing data with polytomous items. It can be concluded that the Bayesian estimation procedure can handle the inequality constraints on the parameters very well. However, the application of Bayesian model selection methods requires more research.     

当结构假设和分布假设不满足时的验证性因子分析：稳健极大似然法估计和贝叶斯估计的比较研究

结构方程模型已被广泛应用于心理学、教育学、以及社会科学领域的统计分析中。结构方程模型分析中最常用的估计方法是基于正 态分布的估计量,比如极大似然估计法。这些方法需要满足两个假设。第一, 理论模型必须正确地反映变量与变量之间的关系,称为结构假 设。第二,数据必须符合多元正态分布,称为分布假设。如果这些假设不满足,基于正态分布的估计量就有可能导致不正确的卡方指数、不 正确的拟合度、以及有偏差的参数估计和参数估计的标准误。在实际应用中,几乎所有的理论模型都不能准确地解释变量与变量之间的关系, 数据也常常呈非多元正态分布。为此,一些新的估计方法得以发展。这些方法要么在理论上不要求数据呈多元正态分布,要么对因数据呈非 正态分布而导致的不正确结果进行纠正。当前较为流行的两种方法是稳健极大似然估计和贝叶斯估计。稳健极大似然估计是应用 Satorra and Bentler (1994) 的方法对不正确的卡方指数和参数估计的标准误进行调整,而参数估计和用极大似然方法得出的完全等同。贝叶斯估计方法则是 基于贝叶斯定理,其要点是：参数的后验分布是由参数的先验分布和数据似然值相乘而得来。后验分布常用马尔科夫蒙特卡洛算法来进行模拟。 对于稳健极大似然估计和贝叶斯估计这两种方法之间的优劣比较,先前的研究只局限于理论模型是正确的情境。而本研究则着重于理论模型 是错误的情境,同时也考虑到数据呈非正态分布的情境。本研究所采用的模型是验证性因子模型,数据全部由计算机模拟而来。数据的生成 取决于三个因素：8 类因子结构,3 种变量分布,和3 组样本量。这三个因素产生72 个模拟条件（72=8x3x3）。每个模拟条件下生成2000 个 数据组,每个数据组都拟合两个模型,一个是正确模型、一个是错误模型。每个模型都用两种估计方法来拟合：稳健极大似然估计法和贝叶 斯估计方法。贝叶斯估计方法中所使用的先验分布是无信息先验分布。结果分析主要着重于模型拒绝率、拟合度、参数估计、和参数估计的 标准误。研究的结果表明：在样本量充足的情况下,两种方法得出的参数估计非常相似。当数据呈非正态分布时,贝叶斯估计法比稳健极大 似然估计法更好地拒绝错误模型。但是,当样本量不足且数据呈正态分布时,贝叶斯估计在拒绝错误模型和参数估计上几乎没有优势,甚至 在一些条件下,比稳健极大似然法要差。     

Approximated adjusted fractional Bayes factors: A general method for testing informative hypotheses

Informative hypotheses are increasingly being used in psychological sciences because they adequately capture researchers’ theories and expectations. In the Bayesian framework, the evaluation of informative hypotheses often makes use of default Bayes factors such as the fractional Bayes factor. This paper approximates and adjusts the fractional Bayes factor such that it can be used to evaluate informative hypotheses in general statistical models. In the fractional Bayes factor a fraction parameter must be specified which controls the amount of information in the data used for specifying an implicit prior. The remaining fraction is used for testing the informative hypotheses. We discuss different choices of this parameter and present a scheme for setting it. Furthermore, a software package is described which computes the approximated adjusted fractional Bayes factor. Using this software package, psychological researchers can evaluate informative hypotheses by means of Bayes factors in an easy manner. Two empirical examples are used to illustrate the procedure.     

Bayesian Inference for Growth Mixture Models with Latent Class Dependent Missing Data

Growth mixture models (GMMs) with nonignorable missing data have drawn increasing attention in research communities but have not been fully studied. The goal of this article is to propose and to evaluate a Bayesian method to estimate the GMMs with latent class dependent missing data. An extended GMM is first presented in which class probabilities depend on some observed explanatory variables and data missingness depends on both the explanatory variables and a latent class variable. A full Bayesian method is then proposed to estimate the model. Through the data augmentation method, conditional posterior distributions for all model parameters and missing data are obtained. A Gibbs sampling procedure is then used to generate Markov chains of model parameters for statistical inference. The application of the model and the method is first demonstrated through the analysis of mathematical ability growth data from the National Longitudinal Survey of Youth 1997 (Bureau of Labor Statistics, U.S. Department of Labor, 1997). A simulation study considering 3 main factors (the sample size, the class probability, and the missing data mechanism) is then conducted and the results show that the proposed Bayesian estimation approach performs very well under the studied conditions. Finally, some implications of this study, including the misspecified missingness mechanism, the sample size, the sensitivity of the model, the number of latent classes, the model comparison, and the future directions of the approach, are discussed.     

A Robust Bayesian Approach for Structural Equation Models with Missing Data

In this paper, normal/independent distributions, including but not limited to the multivariate t distribution, the multivariate contaminated distribution, and the multivariate slash distribution, are used to develop a robust Bayesian approach for analyzing structural equation models with complete or missing data. In the context of a nonlinear structural equation model with fixed covariates, robust Bayesian methods are developed for estimation and model comparison. Results from simulation studies are reported to reveal the characteristics of estimation. The methods are illustrated by using a real data set obtained from diabetes patients.     

Bayesian data analysis as a tool for behavior analysts

Bayesian approaches to data analysis are considered within the context of behavior analysis. The paper distinguishes between Bayesian inference, the use of Bayes Factors, and Bayesian data analysis using specialized tools. Given the importance of prior beliefs to these approaches, the review addresses those situations in which priors have a big effect on the outcome (Bayes Factors) versus a smaller effect (parameter estimation). Although there are many advantages to Bayesian data analysis from a philosophical perspective, in many cases a behavior analyst can be reasonably well‐served by the adoption of traditional statistical tools as long as the focus is on parameter estimation and model comparison, not null hypothesis significance testing. A strong case for Bayesian analysis exists under specific conditions: When prior beliefs can help narrow parameter estimates (an especially important issue given the small sample sizes common in behavior analysis) and when an analysis cannot easily be conducted using traditional approaches (e.g., repeated measures censored regression).     

Hypothesis Testing and Model Comparison in Two-level Structural Equation Models

One basic and important problem in two-level structural equation modeling is to find a good model for the observed sample data. This article demonstrates the use of the well-known Bayes factor in the Bayesian literature for hypothesis testing and model comparison in general two-level structural equation models. It is shown that the proposed methodology is flexible, and can be applied to situations with a wide variety of nonnested models. Moreover, some problems encountered in using existing methods for goodness-of-fit assessment of the proposed model can be alleviated. An illustrative example with some real data from an AIDS care study is presented.     

A Bayesian Approach for Estimating Mediation Effects With Missing Data

Methodologists have developed mediation analysis techniques for a broad range of substantive applications, yet methods for estimating mediating mechanisms with missing data have been understudied. This study outlined a general Bayesian missing data handling approach that can accommodate mediation analyses with any number of manifest variables. Computer simulation studies showed that the Bayesian approach produced frequentist coverage rates and power estimates that were comparable to those of maximum likelihood with the bias-corrected bootstrap. We share an SAS macro that implements Bayesian estimation and use 2 data analysis examples to demonstrate its use.