Extending Integrated Nested Laplace Approximation to a Class of Near‐Gaussian Latent Models

This work extends the integrated nested Laplace approximation (INLA) method to latent models outside the scope of latent Gaussian models, where independent components of the latent field can have a near‐Gaussian distribution. The proposed methodology is an essential component of a bigger project that aims to extend the R package INLA in order to allow the user to add flexibility and challenge the Gaussian assumptions of some of the model components in a straightforward and intuitive way. Our approach is applied to two examples, and the results are compared with that obtained by Markov chain Monte Carlo, showing similar accuracy with only a small fraction of computational time. Implementation of the proposed extension is available in the R‐INLA package.     

A Modification for Bayesian Credible Intervals

In Bayesian analysis, people usually report the highest posterior density (HPD) credible interval as an interval estimate of an unknown parameter. However, when the unknown parameter is the nonnegative normal mean, the Bayesian HPD credible interval under the uniform prior has quite a low minimum frequentist coverage probability. To enhance the minimum frequentist coverage probability of a credible interval, I propose a new method of reporting the Bayesian credible interval. Numerical results show that the new reported credible interval has a much higher minimum frequentist coverage probability than the HPD credible interval.     

Simultaneous Confidence Bands for Linear Regression with Covariates Constrained in Intervals

Abstract. The focus of this article is on simultaneous confidence bands over a rectangular covariate region for a linear regression model with k>1 covariates, for which only conservative or approximate confidence bands are available in the statistical literature stretching back to Working & Hotelling (J. Amer. Statist. Assoc. 24 , 1929; 73–85). Formulas of simultaneous confidence levels of the hyperbolic and constant width bands are provided. These involve only a k‐dimensional integral; it is unlikely that the simultaneous confidence levels can be expressed as an integral of less than k‐dimension. These formulas allow the construction for the first time of exact hyperbolic and constant width confidence bands for at least a small k(>1) by using numerical quadrature. Comparison between the hyperbolic and constant width bands is then addressed under both the average width and minimum volume confidence set criteria. It is observed that the constant width band can be drastically less efficient than the hyperbolic band when k>1. Finally it is pointed out how the methods given in this article can be applied to more general regression models such as fixed‐effect or random‐effect generalized linear regression models.     

Exact Simultaneous Confidence Bands for Quadratic and Cubic Polynomial Regression with Applications in Dose Response Study

Exact simultaneous confidence bands (SCBs) for a polynomial regression model are available only in some special situations. In this paper, simultaneous confidence levels for both hyperbolic and constant width bands for a polynomial function over a given interval are expressed as multidimensional integrals. The dimension of these integrals is equal to the degree of the polynomial. Hence the values can be calculated quickly and accurately via numerical quadrature provided that the degree of the polynomial is small (e.g. 2 or 3). This allows the construction of exact SCBs for quadratic and cubic regression functions over any given interval and for any given design matrix. Quadratic and cubic regressions are frequently used to characterise dose response relationships in addition to many other applications. Comparison between the hyperbolic and constant width bands under both the average width and minimum volume confidence set criteria shows that the constant width band can be much less efficient than the hyperbolic band. For hyperbolic bands, comparison between the exact critical constant and conservative or approximate critical constants indicates that the exact critical constant can be substantially smaller than the conservative or approximate critical constants. Numerical examples from a dose response study are used to illustrate the methods.     

Small sample set estimation of a baseline ranking

Ranking objects by a panel of judges is commonly used in situations where objective attributes cannot easily be measured or interpreted. Under the assumption that the judge independently arrive at their rankings by making pair wise comparisons among the objects in an attempt to reproduce a common baseline ranking w₀, we develop and explore confidence regions and Bayesian highest posterior density credible regions for w₀ with emphasis on very small sample sizes.     

Building and Fitting Non‐Gaussian Latent Variable Models via the Moment‐Generating Function

Abstract. For certain classes of hierarchical models, it is easy to derive an expression for the joint moment‐generating function (MGF) of data, whereas the joint probability density has an intractable form which typically involves an integral. The most important example is the class of linear models with non‐Gaussian latent variables. Parameters in the model can be estimated by approximate maximum likelihood, using a saddlepoint‐type approximation to invert the MGF. We focus on modelling heavy‐tailed latent variables, and suggest a family of mixture distributions that behaves well under the saddlepoint approximation (SPA). It is shown that the well‐known normalization issue renders the ordinary SPA useless in the present context. As a solution we extend the non‐Gaussian leading term SPA to a multivariate setting, and introduce a general rule for choosing the leading term density. The approach is applied to mixed‐effects regression, time‐series models and stochastic networks and it is shown that the modified SPA is very accurate.     

Data-dependent probability matching priors for likelihood ratio and adjusted likelihood ratio statistics

We consider likelihood ratio statistics based on the usual profile likelihood and the standard adjustments thereof proposed in the literature in the presence of nuisance parameters. The role of data-dependent priors in ensuring approximate frequentist validity of posterior credible regions based on the inversion of these statistics is investigated. Unlike what happens with data-free priors, it is seen that the resulting probability matching conditions readily admit solutions which entail approximate frequentist validity of the highest posterior density region as well.     

Bayesian analysis for the two-parameter Pareto distribution based on record values and times

Doostparast and Balakrishnan (Pareto record-based analysis, Statistics, under review) recently developed optimal confidence intervals as well as uniformly most powerful tests for one- and two-sided hypotheses concerning shape and scale parameters, for the two-parameter Pareto distribution based on record data. In this paper, on the basis of record values and inter-record times from the two-parameter Pareto distribution, maximum-likelihood and Bayes estimators as well as credible regions are developed for the two parameters of the Pareto distribution. For illustrative purposes, a data set on annual wages of a sample of production-line workers in a large industrial firm is analysed using the proposed procedures.     

A Case Study for Modelling Cancer Incidence Using Bayesian Spatio‐Temporal Models

Researchers familiar with spatial models are aware of the challenge of choosing the level of spatial aggregation. Few studies have been published on the investigation of temporal aggregation and its impact on inferences regarding disease outcome in space–time analyses. We perform a case study for modelling individual disease outcomes using several Bayesian hierarchical spatio‐temporal models, while taking into account the possible impact of spatial and temporal aggregation. Using longitudinal breast cancer data from South East Queensland, Australia, we consider both parametric and non‐parametric formulations for temporal effects at various levels of aggregation. Two temporal smoothness priors are considered separately; each is modelled with fixed effects for the covariates and an intrinsic conditional autoregressive prior for the spatial random effects. Our case study reveals that different model formulations produce considerably different model performances. For this particular dataset, a classical parametric formulation that assumes a linear time trend produces the best fit among the five models considered. Different aggregation levels of temporal random effects were found to have little impact on model goodness‐of‐fit and estimation of fixed effects.     

Latent Variable Models in Heterogeneous Spaces for Observations of Mixed Types

The maximum likelihood approach to the estimation of factor analytic model parameters most commonly deals with outcomes that are assumed to be multivariate Gaussian random variables in a homogeneous input space. In many practical settings, however, many studies needing factor analytic modeling involve data that, not only are not multivariate Gaussian variables, but also come from a partitioned input space. This article introduces an extension of the maximum likelihood factor analysis that handles multivariate outcomes made up of attributes with different probability distributions, and originating from a partitioned input space. An EM Algorithm combined with Fisher Scoring is used to estimate the parameters of the derived model.     

Simultaneous confidence bands for growth incidence curves in weighted sup-norm metrics

ABSTRACT

The so-called growth incidence curve (GIC) is a popular way to evaluate the distributional pattern of economic growth and pro-poorness of growth in development economics. The log-transformation of the the GIC is related to the sum of empirical quantile processes which allows for constructions of simultaneous confidence bands for the GIC. However, standard constructions of these bands tend to be too wide at the extreme points 0 and 1 because the estimator of the quantile function can be very volatile at the extreme points. In order to construct simultaneous confidence bands which are narrower at the ends, we consider the convergence of quantile processes with weight functions. In particular, we investigate the asymptotic convergence under specific weighted sup-norm metrics and compare different kinds of qualified weight functions. This implies simultaneous confidence bands that are narrower at the boundaries 0 and 1. We show in simulations that these bands have a more regular shape. Finally, we evaluate real data from Uganda with the improved confidence bands.     

Likelihood and bayesian approaches to inference for the stationary point of a quadratic response surface

In response surface analysis, a second order polynomial model is often used for inference on the stationary point of the response function. The standard confidence regions for the stationary point are due to Box & Hunter (1954). The authors propose an alternative parametrization, in which the stationary point is the parameter of interest; likelihood techniques and Bayesian analysis are then easier to perform. The authors also suggest an approximate method to get highest posterior density regions for the maximum point (not simply for the stationary point). Furthermore, they study the coverage probabilities of these Bayesian regions through simulations.     

Empirical Likelihood Inference for the Cox Model with Time-dependent Coefficients via Local Partial Likelihood

Abstract.  The Cox model with time-dependent coefficients has been studied by a number of authors recently. In this paper, we develop empirical likelihood (EL) pointwise confidence regions for the time-dependent regression coefficients via local partial likelihood smoothing. The EL simultaneous confidence bands for a linear combination of the coefficients are also derived based on the strong approximation methods. The EL ratio is formulated through the local partial log-likelihood for the regression coefficient functions. Our numerical studies indicate that the EL pointwise/simultaneous confidence regions/bands have satisfactory finite sample performances. Compared with the confidence regions derived directly based on the asymptotic normal distribution of the local constant estimator, the EL confidence regions are overall tighter and can better capture the curvature of the underlying regression coefficient functions. Two data sets, the gastric cancer data and the Mayo Clinic primary biliary cirrhosis data, are analysed using the proposed method.