Spatial modeling using frequentist approach for disease mapping

In this article, a generalized linear mixed model (GLMM) based on a frequentist approach is employed to examine spatial trend of asthma data. However, the frequentist analysis of GLMM is computationally difficult. On the other hand, the Bayesian analysis of GLMM has been computationally convenient due to the advent of Markov chain Monte Carlo algorithms. Recently developed data cloning (DC) method, which yields to maximum likelihood estimate, provides frequentist approach to complex mixed models and equally computationally convenient method. We use DC to conduct frequentist analysis of spatial models. The advantages of the DC approach are that the answers are independent of the choice of the priors, non-estimable parameters are flagged automatically, and the possibility of improper posterior distributions is completely avoided. We illustrate this approach using a real dataset of asthma visits to hospital in the province of Manitoba, Canada, during 2000–2010. The performance of the DC approach in our application is also studied through a simulation study.     

Prediction in linear mixed models

Following estimation of effects from a linear mixed model, it is often useful to form predicted values for certain factor/variate combinations. The process has been well defined for linear models, but the introduction of random effects into the model means that a decision has to be made about the inclusion or exclusion of random model terms from the predictions. This paper discusses the interpretation of predictions formed including or excluding random terms. Four datasets are used to illustrate circumstances where different prediction strategies may be appropriate: in an orthogonal design, an unbalanced nested structure, a model with cubic smoothing spline terms and for kriging after spatial analysis. The examples also show the need for different weighting schemes that recognize nesting and aliasing during prediction, and the necessity of being able to detect inestimable predictions.     

Monte Carlo approximation of likelihood function in spatial GLMMs through an empirical Bayes method

In spatial generalized linear mixed models (SGLMMs), statistical inference encounters problems, since random effects in the model imply high-dimensional integrals to calculate the marginal likelihood function. In this article, we temporarily treat parameters as random variables and express the marginal likelihood function as a posterior expectation. Hence, the marginal likelihood function is approximated using the obtained samples from the posterior density of the latent variables and parameters given the data. However, in this setting, misspecification of prior distribution of correlation function parameter and problems associated with convergence of Markov chain Monte Carlo (MCMC) methods could have an unpleasant influence on the likelihood approximation. To avoid these challenges, we utilize an empirical Bayes approach to estimate prior hyperparameters. We also use a computationally efficient hybrid algorithm by combining inverse Bayes formula (IBF) and Gibbs sampler procedures. A simulation study is conducted to assess the performance of our method. Finally, we illustrate the method applying a dataset of standard penetration test of soil in an area in south of Iran.     

Comparison of predictions by kriging and spatial autoregressive models

In geostatistics, the prediction of unknown quantities at given locations is commonly made by the kriging technique. In addition to the kriging technique for modeling regular lattice spatial data, the spatial autoregressive models can also be used. In this article, the spatial autoregressive model and the kriging technique are introduced. We extend prediction method proposed by Basu and Reinsel for SAR(2,1) model. Then, using a simulation study and real data, we compare prediction accuracy of the spatial autoregressive models with that of the kriging prediction. The results of simulation study show that predictions made by the autoregressive models are good competitor for the kriging method.     

Random effects selection in generalized linear mixed models via shrinkage penalty function

In this paper, we discuss the selection of random effects within the framework of generalized linear mixed models (GLMMs). Based on a reparametrization of the covariance matrix of random effects in terms of modified Cholesky decomposition, we propose to add a shrinkage penalty term to the penalized quasi-likelihood (PQL) function of the variance components for selecting effective random effects. The shrinkage penalty term is taken as a function of the variance of random effects, initiated by the fact that if the variance is zero then the corresponding variable is no longer random (with probability one). The proposed method takes the advantage of a convenient computation for the PQL estimation and appealing properties for certain shrinkage penalty functions such as LASSO and SCAD. We propose to use a backfitting algorithm to estimate the fixed effects and variance components in GLMMs, which also selects effective random effects simultaneously. Simulation studies show that the proposed approach performs quite well in selecting effective random effects in GLMMs. Real data analysis is made using the proposed approach, too.     

Response prediction in mixed effects models

Although prediction in mixed effects models usually concerns the random effects, in this paper we deal with the problem of prediction of a future, or yet unobserved, response random variable, belonging to a given cluster. In particular, the aim is to define computationally tractable prediction intervals, with conditional and unconditional coverage probability close to the target nominal value. This solution involves the conditional density of the future response random variable given the observed data, or a suitable high-order approximation based on the Laplace method. We prove that, unless the amount of data is very limited, the estimative or naive predictive procedure gives a relatively simple, feasible solution for response prediction. An application to generalized linear mixed models is presented.     

On spatiotemporal prediction for on-line monitoring data

Spatiotemporal prediction is of interest in many areas of applied statistics, especially in environmental monitoring with on-line data information. At first, this article reviews the approaches for spatiotemporal modeling in the context of stochastic processes and then introduces the new class of spatiotemporal dynamic linear models. Further, the methods for linear spatial data analysis, universal kriging and trend surface prediction, are related to the method of spatial linear Bayesian analysis. The Kalman filter is the preferred method for temporal linear Bayesian inferences. By combining the Kalman filter recursions with the trend surface predictor and universal kriging predictor, the prior and posterior spatiotemporal predictors for the observational process are derived, which form the main result of this article. The problem of spatiotemporal linear prediction in the case of unknown first and second order moments is treated as well.     

Theory & Methods: Krige,Smooth, Both or Neither?

Both kriging and non-parametric regression smoothing can model a non-stationary regression function with spatially correlated errors. However comparisons have mainly been based on ordinary kriging and smoothing with uncorrelated errors. Ordinary kriging attributes smoothness of the response to spatial autocorrelation whereas non-parametric regression attributes trends to a smooth regression function. For spatial processes it is reasonable to suppose that the response is due to both trend and autocorrelation. This paper reviews methodology for non-parametric regression with autocorrelated errors which is a natural compromise between the two methods. Re-analysis of the one-dimensional stationary spatial data of Laslett (1994) and a clearly non-stationary time series demonstrates the rather surprising result that for these data, ordinary kriging outperforms more computationally intensive models including both universal kriging and correlated splines for spatial prediction. For estimating the regression function, non-parametric regression provides adaptive estimation, but the autocorrelation must be accounted for in selecting the smoothing parameter.     

An Alternative Estimation Approach for the Heterogeneity Linear Mixed Model

In this article, an alternative estimation approach is proposed to fit linear mixed effects models where the random effects follow a finite mixture of normal distributions. This heterogeneity linear mixed model is an interesting tool since it relaxes the classical normality assumption and is also perfectly suitable for classification purposes, based on longitudinal profiles. Instead of fitting directly the heterogeneity linear mixed model, we propose to fit an equivalent mixture of linear mixed models under some restrictions which is computationally simpler. Unlike the former model, the latter can be maximized analytically using an EM-algorithm and the obtained parameter estimates can be easily used to compute the parameter estimates of interest.     

Bayesian inference for generalized additive mixed models based on Markov random field priors

Most regression problems in practice require flexible semiparametric forms of the predictor for modelling the dependence of responses on covariates. Moreover, it is often necessary to add random effects accounting for overdispersion caused by unobserved heterogeneity or for correlation in longitudinal or spatial data. We present a unified approach for Bayesian inference via Markov chain Monte Carlo simulation in generalized additive and semiparametric mixed models. Different types of covariates, such as the usual covariates with fixed effects, metrical covariates with non-linear effects, unstructured random effects, trend and seasonal components in longitudinal data and spatial covariates, are all treated within the same general framework by assigning appropriate Markov random field priors with different forms and degrees of smoothness. We applied the approach in several case-studies and consulting cases, showing that the methods are also computationally feasible in problems with many covariates and large data sets. In this paper, we choose two typical applications.     

A general joint model for longitudinal measurements and competing risks survival data with heterogeneous random effects

This article studies a general joint model for longitudinal measurements and competing risks survival data. The model consists of a linear mixed effects sub-model for the longitudinal outcome, a proportional cause-specific hazards frailty sub-model for the competing risks survival data, and a regression sub-model for the variance–covariance matrix of the multivariate latent random effects based on a modified Cholesky decomposition. The model provides a useful approach to adjust for non-ignorable missing data due to dropout for the longitudinal outcome, enables analysis of the survival outcome with informative censoring and intermittently measured time-dependent covariates, as well as joint analysis of the longitudinal and survival outcomes. Unlike previously studied joint models, our model allows for heterogeneous random covariance matrices. It also offers a framework to assess the homogeneous covariance assumption of existing joint models. A Bayesian MCMC procedure is developed for parameter estimation and inference. Its performances and frequentist properties are investigated using simulations. A real data example is used to illustrate the usefulness of the approach.     

Approximate bounded influence estimation for longitudinal data with outliers and measurement errors

Mixed effects models or random effects models are popular for the analysis of longitudinal data. In practice, longitudinal data are often complex since there may be outliers in both the response and the covariates and there may be measurement errors. The likelihood method is a common approach for these problems but it can be computationally very intensive and sometimes may even be computationally infeasible. In this article, we consider approximate robust methods for nonlinear mixed effects models to simultaneously address outliers and measurement errors. The approximate methods are computationally very efficient. We show the consistency and asymptotic normality of the approximate estimates. The methods can also be extended to missing data problems. An example is used to illustrate the methods and a simulation is conducted to evaluate the methods.     

Spatio‐temporal modelling of disease mapping of rates

This paper studies generalized linear mixed models (GLMMs) for the analysis of geographic and temporal variability of disease rates. This class of models adopts spatially correlated random effects and random temporal components. Spatio‐temporal models that use conditional autoregressive smoothing across the spatial dimension and autoregressive smoothing over the temporal dimension are developed. The model also accommodates the interaction between space and time. However, the effect of seasonal factors has not been previously addressed and in some applications (e.g., health conditions), these effects may not be negligible. The authors incorporate the seasonal effects of month and possibly year as part of the proposed model and estimate model parameters through generalized estimating equations. The model provides smoothed maps of disease risk and eliminates the instability of estimates in low‐population areas while maintaining geographic resolution. They illustrate the approach using a monthly data set of the number of asthma presentations made by children to Emergency Departments (EDs) in the province of Alberta, Canada, during the period 2001–2004. The Canadian Journal of Statistics 38: 698–715; 2010 © 2010 Statistical Society of Canada     

Constructing and fitting models for cokriging and multivariable spatial prediction

We consider best linear unbiased prediction for multivariable data. Minimizing mean-squared-prediction errors leads to prediction equations involving either covariances or variograms. We discuss problems with multivariate extensions that include the construction of valid models and the estimation of their parameters. In this paper, we develop new methods to construct valid crossvariograms, fit them to data, and then use them for multivariable spatial prediction, including cokriging. Crossvariograms are constructed by explicitly modeling spatial data as moving averages over white noise random processes. Parameters of the moving average functions may be inferred from the variogram, and with few additional parameters, crossvariogram models are constructed. Weighted least squares is then used to fit the crossvariogram model to the empirical crossvariogram for the data. We demonstrate the method for simulated data, and show a considerable advantage of cokriging over ordinary kriging.     

Incomplete covariates data in generalized linear models

We consider regression analysis when part of covariates are incomplete in generalized linear models. The incomplete covariates could be due to measurement error or missing for some study subjects. We assume there exists a validation sample in which the data is complete and is a simple random subsample from the whole sample. Based on the idea of projection-solution method in Heyde (1997, Quasi-Likelihood and its Applications: A General Approach to Optimal Parameter Estimation. Springer, New York), a class of estimating functions is proposed to estimate the regression coefficients through the whole data. This method does not need to specify a correct parametric model for the incomplete covariates to yield a consistent estimate, and avoids the ‘curse of dimensionality’ encountered in the existing semiparametric method. Simulation results shows that the finite sample performance and efficiency property of the proposed estimates are satisfactory. Also this approach is computationally convenient hence can be applied to daily data analysis.     

Estimation in large cross random-effect models by data augmentation

Estimation in mixed linear models is, in general, computationally demanding, since applied problems may involve extensive data sets and large numbers of random effects. Existing computer algorithms are slow and/or require large amounts of memory. These problems are compounded in generalized linear mixed models for categorical data, since even approximate methods involve fitting of a linear mixed model within steps of an iteratively reweighted least squares algorithm. Only in models in which the random effects are hierarchically nested can the computations for fitting these models to large data sets be carried out rapidly. We describe a data augmentation approach to these computational difficulties in which we repeatedly fit an overlapping series of submodels, incorporating the missing terms in each submodel as 'offsets'. The submodels are chosen so that they have a nested random-effect structure, thus allowing maximum exploitation of the computational efficiency which is available in this case. Examples of the use of the algorithm for both metric and discrete responses are discussed, all calculations being carried out using macros within the MLwiN program.     

Comparison of designs for generalized linear models under model misspecification

The purpose of this article is to demonstrate the use of the quantile dispersion graphs (QDGs) approach for comparing candidate designs for generalized linear models in the presence of model misspecification in the linear predictor. The proposed design criterion is based on the mean-squared error of prediction which incorporates the prediction variance and the bias caused by fitting the wrong model. The method of kriging is used to estimate the unknown function assumed to be the cause of model misspecification. The QDGs approach is also useful in assessing the robustness of a given design to values of the unknown parameters in the linear predictor. Three numerical examples are presented to illustrate the application of the proposed methodology.     

Spatial generalized linear mixed models in small area estimation

In survey sampling, policy decisions regarding the allocation of resources to sub‐groups of a population depend on reliable predictors of their underlying parameters. However, in some sub‐groups, called small areas due to small sample sizes relative to the population, the information needed for reliable estimation is typically not available. Consequently, data on a coarser scale are used to predict the characteristics of small areas. Mixed models are the primary tools in small area estimation (SAE) and also borrow information from alternative sources (e.g., previous surveys and administrative and census data sets). In many circumstances, small area predictors are associated with location. For instance, in the case of chronic disease or cancer, it is important for policy makers to understand spatial patterns of disease in order to determine small areas with high risk of disease and establish prevention strategies. The literature considering SAE with spatial random effects is sparse and mostly in the context of spatial linear mixed models. In this article, small area models are proposed for the class of spatial generalized linear mixed models to obtain small area predictors and corresponding second‐order unbiased mean squared prediction errors via Taylor expansion and a parametric bootstrap approach. The performance of the proposed approach is evaluated through simulation studies and application of the models to a real esophageal cancer data set from Minnesota, U.S.A. The Canadian Journal of Statistics 47: 426–437; 2019 © 2019 Statistical Society of Canada     

Approximate composite marginal likelihood inference in spatial generalized linear mixed models

Non-Gaussian spatial responses are usually modeled using spatial generalized linear mixed model with spatial random effects. The likelihood function of this model cannot usually be given in a closed form, thus the maximum likelihood approach is very challenging. There are numerical ways to maximize the likelihood function, such as Monte Carlo Expectation Maximization and Quadrature Pairwise Expectation Maximization algorithms. They can be applied but may in such cases be computationally very slow or even prohibitive. Gauss–Hermite quadrature approximation only suitable for low-dimensional latent variables and its accuracy depends on the number of quadrature points. Here, we propose a new approximate pairwise maximum likelihood method to the inference of the spatial generalized linear mixed model. This approximate method is fast and deterministic, using no sampling-based strategies. The performance of the proposed method is illustrated through two simulation examples and practical aspects are investigated through a case study on a rainfall data set.     

The Effect of Leap Years and Seasonal Trends on the Birthday Problem

Most data have a space and time label associated with them; data that are close together are usually more correlated than those that are far apart. Prediction (or forecasting) of a process at a particular label where there is no datum, from observed nearby data, is the subject of this article. One approach, known as geostatistics, is featured, from which linear methods of spatial prediction (kriging) will be considered. Brief reference is made to other linear/nonlinear, stochastic/deterministic predictors. The (linear) geostatistical method is applied to piezometric-head data around a potential nuclear-waste repository site.