A Bayesian Model for Markov Chains via Jeffrey's Prior

Abstract

This work deals with the problem of Bayesian estimation of the transition probabilities associated with multistate Markov chain. The model is based on the Jeffreys' noninformative prior. The Bayesian estimator is approximated by means of MCMC techniques. A numerical study by simulation is done in order to compare the Bayesian estimator with the maximum likelihood estimator.     

A default Bayesian procedure for the generalized Pareto distribution

The generalized Pareto distribution is used to model the exceedances over a threshold in a number of fields, including the analysis of environmental extreme events and financial data analysis. We use this model in a default Bayesian framework where no prior information is available on unknown model parameters. Using a large simulation study, we compare the performance of our posterior estimations of parameters with other methods proposed in the literature. We show that our procedure also allows to make inferences in other quantities of interest in extreme value analysis without asymptotic arguments. We apply the proposed methodology to a real data set.     

Objective Bayesian multiple comparisons for normal variances

This paper considers the multiple comparisons problem for normal variances. We propose a solution based on a Bayesian model selection procedure to this problem in which no subjective input is considered. We construct the intrinsic and fractional priors for which the Bayes factors and model selection probabilities are well defined. The posterior probability of each model is used as a model selection tool. The behaviour of these Bayes factors is compared with the Bayesian information criterion of Schwarz and some frequentist tests.     

On Variance Components in Semiparametric Mixed Models for Longitudinal Data

Abstract. First, to test the existence of random effects in semiparametric mixed models (SMMs) under only moment conditions on random effects and errors, we propose a very simple and easily implemented non‐parametric test based on a difference between two estimators of the error variance. One test is consistent only under the null and the other can be so under both the null and alternatives. Instead of erroneously solving the non‐standard two‐sided testing problem, as in most papers in the literature, we solve it correctly and prove that the asymptotic distribution of our test statistic is standard normal. This avoids Monte Carlo approximations to obtain p ‐values, as is needed for many existing methods, and the test can detect local alternatives approaching the null at rates up to root n. Second, as the higher moments of the error are necessarily estimated because the standardizing constant involves these quantities, we propose a general method to conveniently estimate any moments of the error. Finally, a simulation study and a real data analysis are conducted to investigate the properties of our procedures.     

Bayesian Analysis of Nonlinear Reproductive Dispersion Mixed Models for Longitudinal Data with Nonignorable Missing Covariates

This article proposes a Bayesian approach, which can simultaneously obtain the Bayesian estimates of unknown parameters and random effects, to analyze nonlinear reproductive dispersion mixed models (NRDMMs) for longitudinal data with nonignorable missing covariates and responses. The logistic regression model is employed to model the missing data mechanisms for missing covariates and responses. A hybrid sampling procedure combining the Gibber sampler and the Metropolis-Hastings algorithm is presented to draw observations from the conditional distributions. Because missing data mechanism is not testable, we develop the logarithm of the pseudo-marginal likelihood, deviance information criterion, the Bayes factor, and the pseudo-Bayes factor to compare several competing missing data mechanism models in the current considered NRDMMs with nonignorable missing covaraites and responses. Three simulation studies and a real example taken from the paediatric AIDS clinical trial group ACTG are used to illustrate the proposed methodologies. Empirical results show that our proposed methods are effective in selecting missing data mechanism models.     

Bayesian computation for Log-Gaussian Cox processes: a comparative analysis of methods

The Log-Gaussian Cox process is a commonly used model for the analysis of spatial point pattern data. Fitting this model is difficult because of its doubly stochastic property, that is, it is a hierarchical combination of a Poisson process at the first level and a Gaussian process at the second level. Various methods have been proposed to estimate such a process, including traditional likelihood-based approaches as well as Bayesian methods. We focus here on Bayesian methods and several approaches that have been considered for model fitting within this framework, including Hamiltonian Monte Carlo, the Integrated nested Laplace approximation, and Variational Bayes. We consider these approaches and make comparisons with respect to statistical and computational efficiency. These comparisons are made through several simulation studies as well as through two applications, the first examining ecological data and the second involving neuroimaging data.     

The use of local and nonlocal priors in Bayesian test-based monitoring for single-arm phase II clinical trials

Bayesian sequential monitoring is widely used in adaptive phase II studies where the objective is to examine whether an experimental drug is efficacious. Common approaches for Bayesian sequential monitoring are based on posterior or predictive probabilities and Bayesian hypothesis testing procedures using Bayes factors. In the first part of the paper, we briefly show the connections between test-based (TB) and posterior probability-based (PB) sequential monitoring approaches. Next, we extensively investigate the choice of local and nonlocal priors for the TB monitoring procedure. We describe the pros and cons of different priors in terms of operating characteristics. We also develop a user-friendly Shiny application to implement the TB design.     

Bayesian hypothesis testing for selected regression coefficients

ABSTRACT

We develop new Bayesian regression tests for prespecified regression coefficients. Simple, closed forms of the Bayes factors are derived that depend only on the regression t-statistic and F-statistic and the usual associated t and F distributions. The priors that allow those forms are simple and also meaningful, requiring minimal but practically important subjective inputs.     

Approximation of power in multivariate analysis

We consider the calculation of power functions in classical multivariate analysis. In this context, power can be expressed in terms of tail probabilities of certain noncentral distributions. The necessary noncentral distribution theory was developed between the 1940s and 1970s by a number of authors. However, tractable methods for calculating the relevant probabilities have been lacking. In this paper we present simple yet extremely accurate saddlepoint approximations to power functions associated with the following classical test statistics: the likelihood ratio statistic for testing the general linear hypothesis in MANOVA; the likelihood ratio statistic for testing block independence; and Bartlett's modified likelihood ratio statistic for testing equality of covariance matrices.     

Bayesian inference for the randomly censored Weibull distribution

In this paper, we consider the Bayesian inference of the unknown parameters of the randomly censored Weibull distribution. A joint conjugate prior on the model parameters does not exist; we assume that the parameters have independent gamma priors. Since closed-form expressions for the Bayes estimators cannot be obtained, we use Lindley's approximation, importance sampling and Gibbs sampling techniques to obtain the approximate Bayes estimates and the corresponding credible intervals. A simulation study is performed to observe the behaviour of the proposed estimators. A real data analysis is presented for illustrative purposes.     

A bayesian approach for testing periodicity of dichotomous observations

A Bayesian approach is utilized to test for periodicity in a dichotomous time series. Dichotomous data arise in a variety of circumstances when a variable takes on only two possible values. Conjugate and noninformative priors are considered as well as a hierarchical Bayes approach; the latter is considered the superior Bayes methodology. The situation of stochastic period lengths is also discussed. The generalization to the multinomial model is investigated to allow for the case that a variable takes on more than two possible values. In all cases decisions are made based on a Bayes factor. The proposed procedures are demonstrated on earthquake data in the central Virginia seismic zone     

Classical and Bayesian estimation of P(Y < X) for Kumaraswamy's distribution

The aim of this paper is to study the estimation of the reliability R=P(Y<X) when X and Y are independent random variables that follow Kumaraswamy's distribution with different parameters. If we assume that the first shape parameter is common and known, the maximum-likelihood estimator (MLE), the exact confidence interval and the uniformly minimum variance unbiased estimator of R are obtained. Moreover, when the first parameter is common but unknown, MLEs, Bayes estimators, asymptotic distributions and confidence intervals for R are derived. Furthermore, Bayes and empirical Bayes estimators for R are obtained when the first parameter is common and known. Finally, when all four parameters are different and unknown, the MLE of R is obtained. Monte Carlo simulations are performed to compare the different proposed methods and conclusions on the findings are given.     

Bayesian t-tests for correlations and partial correlations

In this paper, we develop Bayes factor based testing procedures for the presence of a correlation or a partial correlation. The proposed Bayesian tests are obtained by restricting the class of the alternative hypotheses to maximize the probability of rejecting the null hypothesis when the Bayes factor is larger than a specified threshold. It turns out that they depend simply on the frequentist t-statistics with the associated critical values and can thus be easily calculated by using a spreadsheet in Excel and in fact by just adding one more step after one has performed the frequentist correlation tests. In addition, they are able to yield an identical decision with the frequentist paradigm, provided that the evidence threshold of the Bayesian tests is determined by the significance level of the frequentist paradigm. We illustrate the performance of the proposed procedures through simulated and real-data examples.     

A Test for Multivariate Analysis of Variance in High Dimension

In this article, we consider the problem of testing a general multivariate linear hypothesis in a multivariate linear model when the N × p observation matrix is normally distributed with unknown covariance matrix, and N ≤ p. This includes the case of testing the equality of several mean vectors. A test is proposed which is a generalized version of the two-sample test proposed by Srivastava and Du (2008 Srivastava , M. S. , Du , M. ( 2008 ). A test for the mean vector with fewer observations than the dimension . J. Multivariate Anal. 99 : 386 – 402 .[Crossref], [Web of Science ®] , [Google Scholar]). The asymptotic null and nonnull distributions are obtained. The performance of this test is compared, theoretically as well as numerically, with the corresponding generalized version of the two-sample Dempster (1958 Dempster , A. P. (1958). A high dimensional two sample significance test. Ann. Math. Statist. 29:995–1010.[Crossref] , [Google Scholar]) test, or more appropriately Bai and Saranadasa (1996 Bai , Z. , Saranadasa , H. ( 1996 ). Effect of high dimension: an example of a two sample problem . Statistica Sinica 6 : 311 – 329 .[Web of Science ®] , [Google Scholar]) test who gave its asymptotic version.     

Estimation and prediction for spatial generalized linear mixed models using high order Laplace approximation

Estimation and prediction in generalized linear mixed models are often hampered by intractable high dimensional integrals. This paper provides a framework to solve this intractability, using asymptotic expansions when the number of random effects is large. To that end, we first derive a modified Laplace approximation when the number of random effects is increasing at a lower rate than the sample size. Second, we propose an approximate likelihood method based on the asymptotic expansion of the log-likelihood using the modified Laplace approximation which is maximized using a quasi-Newton algorithm. Finally, we define the second order plug-in predictive density based on a similar expansion to the plug-in predictive density and show that it is a normal density. Our simulations show that in comparison to other approximations, our method has better performance. Our methods are readily applied to non-Gaussian spatial data and as an example, the analysis of the rhizoctonia root rot data is presented.     

Bayesian estimation and prediction for Weibull model with progressive censoring

This article presents the statistical inferences on Weibull parameters with the data that are progressively type II censored. The maximum likelihood estimators are derived. For incorporation of previous information with current data, the Bayesian approach is considered. We obtain the Bayes estimators under squared error loss with a bivariate prior distribution, and derive the credible intervals for the parameters of Weibull distribution. Also, the Bayes prediction intervals for future observations are obtained in the one- and two-sample cases. The method is shown to be practical, although a computer program is required for its implementation. A numerical example is presented for illustration and some simulation study are performed.     

Marginal likelihood estimation from the Metropolis output: tips and tricks for efficient implementation in generalized linear latent variable models

The marginal likelihood can be notoriously difficult to compute, and particularly so in high-dimensional problems. Chib and Jeliazkov employed the local reversibility of the Metropolis–Hastings algorithm to construct an estimator in models where full conditional densities are not available analytically. The estimator is free of distributional assumptions and is directly linked to the simulation algorithm. However, it generally requires a sequence of reduced Markov chain Monte Carlo runs which makes the method computationally demanding especially in cases when the parameter space is large. In this article, we study the implementation of this estimator on latent variable models which embed independence of the responses to the observables given the latent variables (conditional or local independence). This property is employed in the construction of a multi-block Metropolis-within-Gibbs algorithm that allows to compute the estimator in a single run, regardless of the dimensionality of the parameter space. The counterpart one-block algorithm is also considered here, by pointing out the difference between the two approaches. The paper closes with the illustration of the estimator in simulated and real-life data sets.     

The Role of Posterior Densities in Latent Variable Models for Ordinal Data

In latent variable models, problems related to the integration of the likelihood function arise since analytical solutions do not exist. Laplace and Adaptive Gauss-Hermite (AGH) approximations have been discussed as good approximating methods. Their performance relies on the assumption of normality of the posterior density of the latent variables, but, in small samples, this is not necessarily assured. Here, we analyze how the shape of the posterior densities varies as function of the model parameters, and we investigate its influence on the performance of AGH and of the Laplace approximation.     

Bayesian inference of three-parameter bathtub-shaped lifetime distribution

We investigate a Bayesian inference in the three-parameter bathtub-shaped lifetime distribution which is obtained by adding a power parameter to the two-parameter bathtub-shaped lifetime distribution suggested by Chen (2000). The Bayes estimators under the balanced squared error loss function are derived for three parameters. Then, we have used Lindley's and Tierney–Kadane approximations (see Lindley 1980; Tierney and Kadane 1986) for computing these Bayes estimators. In particular, we propose the explicit form of Lindley's approximation for the model with three parameters. We also give applications with a simulated data set and two real data sets to show the use of discussed computing methods. Finally, concluding remarks are mentioned.     

A Note on Bartlett's M Test for Homogeneity of Variances

After pointing out a drawback in Bartlett's chi-square approximation, we suggest a simple modification and a Gamma approximation to improve Bartlett's M test for homogeneity of variances.