Evaluation of Bayesian multiple stage estimation under spatial CAR model variants

In this study, an evaluation of Bayesian hierarchical models is made based on simulation scenarios to compare single-stage and multi-stage Bayesian estimations. Simulated datasets of lung cancer disease counts for men aged 65 and older across 44 wards in the London Health Authority were analysed using a range of spatially structured random effect components. The goals of this study are to determine which of these single-stage models perform best given a certain simulating model, how estimation methods (single- vs. multi-stage) compare in yielding posterior estimates of fixed effects in the presence of spatially structured random effects, and finally which of two spatial prior models – the Leroux or ICAR model, perform best in a multi-stage context under different assumptions concerning spatial correlation. Among the fitted single-stage models without covariates, we found that when there is low amount of variability in the distribution of disease counts, the BYM model is relatively robust to misspecification in terms of DIC, while the Leroux model is the least robust to misspecification. When these models were fit to data generated from models with covariates, we found that when there was one set of covariates – either spatially correlated or non-spatially correlated, changing the values of the fixed coefficients affected the ability of either the Leroux or ICAR model to fit the data well in terms of DIC. When there were multiple sets of spatially correlated covariates in the simulating model, however, we could not distinguish the goodness of fit to the data between these single-stage models. We found that the multi-stage modelling process via the Leroux and ICAR models generally reduced the variance of the posterior estimated fixed effects for data generated from models with covariates and a UH term compared to analogous single-stage models. Finally, we found the multi-stage Leroux model compares favourably to the multi-stage ICAR model in terms of DIC. We conclude that the mutli-stage Leroux model should be seriously considered in applications of Bayesian disease mapping when an investigator desires to fit a model with both fixed effects and spatially structured random effects to Poisson count data.     

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     

A Bayesian kriged Kalman model for short-term forecasting of air pollution levels

Summary.  Short-term forecasts of air pollution levels in big cities are now reported in news-papers and other media outlets. Studies indicate that even short-term exposure to high levels of an air pollutant called atmospheric particulate matter can lead to long-term health effects. Data are typically observed at fixed monitoring stations throughout a study region of interest at different time points. Statistical spatiotemporal models are appropriate for modelling these data. We consider short-term forecasting of these spatiotemporal processes by using a Bayesian kriged Kalman filtering model. The spatial prediction surface of the model is built by using the well-known method of kriging for optimum spatial prediction and the temporal effects are analysed by using the models underlying the Kalman filtering method. The full Bayesian model is implemented by using Markov chain Monte Carlo techniques which enable us to obtain the optimal Bayesian forecasts in time and space. A new cross-validation method based on the Mahalanobis distance between the forecasts and observed data is also developed to assess the forecasting performance of the model implemented.     

Testing the Goodness of Fit of Parametric Regression Models with Random Toeplitz Forms

ABSTRACT: We introduce a class of Toeplitz‐band matrices for simple goodness of fit tests for parametric regression models. For a given length r of the band matrix the asymptotic optimal solution is derived. Asymptotic normality of the corresponding test statistic is established under a fixed and random design assumption as well as for linear and non‐linear models, respectively. This allows testing at any parametric assumption as well as the computation of confidence intervals for a quadratic measure of discrepancy between the parametric model and the true signal g;. Furthermore, the connection between testing the parametric goodness of fit and estimating the error variance is highlighted. As a by‐product we obtain a much simpler proof of a result of 34 ) concerning the optimality of an estimator for the variance. Our results unify and generalize recent results by 9 ) and 15 , 16 ) in several directions. Extensions to multivariate predictors and unbounded signals are discussed. A simulation study shows that a simple jacknife correction of the proposed test statistics leads to reasonable finite sample approximations.     

A semiparametric stochastic mixed effects model for bivariate cyclic longitudinal data

We propose a flexible semiparametric stochastic mixed effects model for bivariate cyclic longitudinal data. The model can handle either single cycle or, more generally, multiple consecutive cycle data. The approach models the mean of responses by parametric fixed effects and a smooth nonparametric function for the underlying time effects, and the relationship across the bivariate responses by a bivariate Gaussian random field and a joint distribution of random effects. The proposed model not only can model complicated individual profiles, but also allows for more flexible within-subject and between-response correlations. The fixed effects regression coefficients and the nonparametric time functions are estimated using maximum penalized likelihood, where the resulting estimator for the nonparametric time function is a cubic smoothing spline. The smoothing parameters and variance components are estimated simultaneously using restricted maximum likelihood. Simulation results show that the parameter estimates are close to the true values. The fit of the proposed model on a real bivariate longitudinal dataset of pre-menopausal women also performs well, both for a single cycle analysis and for a multiple consecutive cycle analysis. The Canadian Journal of Statistics 48: 471–498; 2020 © 2020 Statistical Society of Canada     

Evaluation of some random effects methodology applicable to bird ringing data

Existing models for ring recovery and recapture data analysis treat temporal variations in annual survival probability (S) as fixed effects. Often there is no explainable structure to the temporal variation in S 1 , … , S k ; random effects can then be a useful model: Si = E(S) + k i . Here, the temporal variation in survival probability is treated as random with average value E( k 2 ) = σ 2 . This random effects model can now be fit in program MARK. Resultant inferences include point and interval estimation for process variation, σ 2 , estimation of E(S) and var(Ê(S)) where the latter includes a component for σ 2 as well as the traditional component for v ar(S|S). Furthermore, the random effects model leads to shrinkage estimates, S i , as improved (in mean square error) estimators of Si compared to the MLE, S i , from the unrestricted time-effects model. Appropriate confidence intervals based on the S i are also provided. In addition, AIC has been generalized to random effects models. This paper presents results of a Monte Carlo evaluation of inference performance under the simple random effects model. Examined by simulation, under the simple one group Cormack-Jolly-Seber (CJS) model, are issues such as bias of σ 2 , confidence interval coverage on σ 2 , coverage and mean square error comparisons for inference about Si based on shrinkage versus maximum likelihood estimators, and performance of AIC model selection over three models: S i = S (no effects), Si = E(S) + k i (random effects), and S 1 , … , S k (fixed effects). For the cases simulated, the random effects methods performed well and were uniformly better than fixed effects MLE for the S i .     

A Lack-of-Fit Test for Heteroscedastic Regression Models via Cosine-Series Smoothers

In this paper, a test is derived to assess the validity of heteroscedastic nonlinear regression models by a non‐parametric cosine regression method. For order selection, the paper proposes a data‐driven method that uses the parametric null model optimal order. This method yields a test that is asymptotically normally distributed under the null hypothesis and is consistent against any fixed alternative. Simulation studies that test the lack of fit of a generalized linear model are conducted to compare the performance of the proposed test with that of an existing non‐parametric kernel test. A dataset of esterase levels is used to demonstrate the proposed method in practice.     

Improved estimation procedures for multilevel models with binary response: a case-study

During recent years, analysts have been relying on approximate methods of inference to estimate multilevel models for binary or count data. In an earlier study of random-intercept models for binary outcomes we used simulated data to demonstrate that one such approximation, known as marginal quasi-likelihood, leads to a substantial attenuation bias in the estimates of both fixed and random effects whenever the random effects are non-trivial. In this paper, we fit three-level random-intercept models to actual data for two binary outcomes, to assess whether refined approximation procedures, namely penalized quasi-likelihood and second-order improvements to marginal and penalized quasi-likelihood, also underestimate the underlying parameters. The extent of the bias is assessed by two standards of comparison: exact maximum likelihood estimates, based on a Gauss–Hermite numerical quadrature procedure, and a set of Bayesian estimates, obtained from Gibbs sampling with diffuse priors. We also examine the effectiveness of a parametric bootstrap procedure for reducing the bias. The results indicate that second-order penalized quasi-likelihood estimates provide a considerable improvement over the other approximations, but all the methods of approximate inference result in a substantial underestimation of the fixed and random effects when the random effects are sizable. We also find that the parametric bootstrap method can eliminate the bias but is computationally very intensive.     

Chi-Squared Goodness-of-Fit Tests for Parametric Accelerated Failure Time Models

We give chi-squared goodness-of fit tests for parametric regression models such as accelerated failure time, proportional hazards, generalized proportional hazards, frailty models, transformation models, and models with cross-effects of survival functions. Random right censored data are used. Choice of random grouping intervals as data functions is considered.     

Hierarchical overdispersed Poisson model with macrolevel autocorrelation

We review Bayesian analysis of hierarchical non-standard Poisson regression models with an emphasis on microlevel heterogeneity and macrolevel autocorrelation. For the former case, we confirm that negative binomial regression usually accounts for microlevel heterogeneity (overdispersion) satisfactorily; for the latter case, we apply the simple first-order Markov transition model to conveniently capture the macrolevel autocorrelation which often arises from temporal and/or spatial count data, rather than attaching complex random effects directly to the regression parameters. Specifically, we extend the hierarchical (multilevel) Poisson model into negative binomial models with macrolevel autocorrelation using restricted gamma mixture with unit mean and Markov transition covariate created from preceding residuals. We prove a mild sufficient condition for posterior propriety under flat prior for the interesting fixed effects. Our methodology is implemented by analyzing the Baltic sea peracarids diurnal activity data published in the marine biology and ecology literature.     

A Class of Convolution‐Based Models for Spatio‐Temporal Processes with Non‐Separable Covariance Structure

Abstract. In this article, we propose a new parametric family of models for real‐valued spatio‐temporal stochastic processes S ( x , t ) and show how low‐rank approximations can be used to overcome the computational problems that arise in fitting the proposed class of models to large datasets. Separable covariance models, in which the spatio‐temporal covariance function of S ( x , t ) factorizes into a product of purely spatial and purely temporal functions, are often used as a convenient working assumption but are too inflexible to cover the range of covariance structures encountered in applications. We define positive and negative non‐separability and show that in our proposed family we can capture positive, zero and negative non‐separability by varying the value of a single parameter.     

Non parametric space-time modeling of SO2 in presence of many missing data

Given pollution measurement from a network of monitoring sites in the area of a city and over an extended period of time, an important problem is to identify the spatial and temporal structure of the data. In this paper we focus on the identification and estimate of a statistical non parametric model to analyse the SO₂ in the city of Padua, where data are collected by some fixed stations and some mobile stations moving without any specific rule in different new locations. The impact of the use of mobile stations is that for each location there are times when data was not collected. Assuming temporal stationarity and spatial isotropy for the residuals of an additive model for the logarithm of SO₂ concentration, we estimate the semivariogram using a kernel-type estimator. Attempts are made to avoid the assumption of spatial isotropy. Bootstrap confidence bands are obtained for the spatial component of the additive model that is a deterministic function which defines the spatial structure. Finally, an example is proposed to design an optimal network for the mobiles monitoring stations in a fixed future time, given all the information available.     

Weighted re‐randomization tests for minimization with unbalanced allocation

Re‐randomization test has been considered as a robust alternative to the traditional population model‐based methods for analyzing randomized clinical trials. This is especially so when the clinical trials are randomized according to minimization, which is a popular covariate‐adaptive randomization method for ensuring balance among prognostic factors. Among various re‐randomization tests, fixed‐entry‐order re‐randomization is advocated as an effective strategy when a temporal trend is suspected. Yet when the minimization is applied to trials with unequal allocation, fixed‐entry‐order re‐randomization test is biased and thus compromised in power. We find that the bias is due to non‐uniform re‐allocation probabilities incurred by the re‐randomization in this case. We therefore propose a weighted fixed‐entry‐order re‐randomization test to overcome the bias. The performance of the new test was investigated in simulation studies that mimic the settings of a real clinical trial. The weighted re‐randomization test was found to work well in the scenarios investigated including the presence of a strong temporal trend. Copyright © 2013 John Wiley & Sons, Ltd.     

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     

Spatial modelling of the two‐party preferred vote in Australian federal elections: 2001–2016

We examine the relationships between electoral socio‐demographic characteristics and two‐party preferences in the six Australian federal elections held between 2001 and 2016. Socio‐demographic information is derived from the Australian Census which occurs every 5 years. Since a census is not directly available for each election, an imputation method is employed to estimate census data for the electorates at the time of each election. This accounts for both spatial and temporal changes in electoral characteristics between censuses. To capture any spatial heterogeneity, a spatial error model is estimated for each election, which incorporates a spatially structured random effect vector. Over time, the impact of most socio‐demographic characteristics that affect electoral two‐party preference do not vary, with age distribution, industry of work, incomes, household mobility and relationships having strong effects in each of the six elections. Education and unemployment are among those that have varying effects. All data featured in this study have been contributed to the eechidna R package (available on CRAN).     

Generalised quasi‐likelihood inference in a semi‐parametric binary dynamic mixed logit model

There exists a recent study where dynamic mixed‐effects regression models for count data have been extended to a semi‐parametric context. However, when one deals with other discrete data such as binary responses, the results based on count data models are not directly applicable. In this paper, we therefore begin with existing binary dynamic mixed models and generalise them to the semi‐parametric context. For inference, we use a new semi‐parametric conditional quasi‐likelihood (SCQL) approach for the estimation of the non‐parametric function involved in the semi‐parametric model, and a semi‐parametric generalised quasi‐likelihood (SGQL) approach for the estimation of the main regression, dynamic dependence and random effects variance parameters. A semi‐parametric maximum likelihood (SML) approach is also used as a comparison to the SGQL approach. The properties of the estimators are examined both asymptotically and empirically. More specifically, the consistency of the estimators is established and finite sample performances of the estimators are examined through an intensive simulation study.     

Bayesian space-time modeling of malaria incidence in Sucre state, Venezuela

Malaria is a parasitic infectious tropical disease that causes high mortality rates in the tropical belt. In Venezuela, Sucre state is considered the third state with most disease prevalence. This paper presents a hierarchical regression log-Poisson space-time model within a Bayesian approach to represent the incidence of malaria in Sucre state, Venezuela, during the period 1990–2002 in 15 municipalities of the state. Several additive models for the logarithm of the relative risk of the disease for each district were considered. These models differ in their structure by including different combinations of social-economic and climatic covariates in a multiple regression term. A random effect that captures the spatial heterogeneity in the study region, and a CAR (Conditionally Autoregressive) component that recognizes the effect of nearby municipalities in the transmission of the disease each year, are also included in the model. A simpler version without including the CAR component was also fitted to the data. Model estimation and predictive inference was carried out through the implementation of a computer code in the WinBUGS software, which makes use of Markov Chain Monte Carlo (MCMC) methods. For model selection the criterion of minimum posterior predictive loss (D) was used. The Moran I statistic was calculated to test the independence of the residuals of the resulting model. Finally, we verify the model fit by using the Bayesian p-value, and in most cases the selected model captures the spatial structure of the relative risks among the neighboring municipalities each year. For years with a poor model fit, the t-Student distribution is used as an alternative model for the spatial local random effect with better fit to the tail behavior of the data probability distribution.     

Testing Goodness of Fit of Parametric AFT and PH Models with Residuals

In this article, we consider the problems of testing the goodness of fit of the parametric accelerated failure time model and the Cox proportional hazards model. We consider omnibus test statistics based on residuals. The statistical distributions of Kolmogorov, Cramer-von Mises–Smirnov, and Anderson–Darling statistics are all investigated by means of Monte Carlo simulations. Type-I, Type-II, and independent random censoring situations are all considered in this study. A Monte Carlo power study has also been carried out for these tests to distinguish between various baseline models, which reveals that the Anderson–Darling test performs better than the others.     

A Cox‐Aalen Model for Interval‐censored Data

The Cox‐Aalen model, obtained by replacing the baseline hazard function in the well‐known Cox model with a covariate‐dependent Aalen model, allows for both fixed and dynamic covariate effects. In this paper, we examine maximum likelihood estimation for a Cox‐Aalen model based on interval‐censored failure times with fixed covariates. The resulting estimator globally converges to the truth slower than the parametric rate, but its finite‐dimensional component is asymptotically efficient. Numerical studies show that estimation via a constrained Newton method performs well in terms of both finite sample properties and processing time for moderate‐to‐large samples with few covariates. We conclude with an application of the proposed methods to assess risk factors for disease progression in psoriatic arthritis.     

Hierarchical Generalized Linear Models and Frailty Models with Bayesian Nonparametric Mixing

This paper proposes Bayesian nonparametric mixing for some well-known and popular models. The distribution of the observations is assumed to contain an unknown mixed effects term which includes a fixed effects term, a function of the observed covariates, and an additive or multiplicative random effects term. Typically these random effects are assumed to be independent of the observed covariates and independent and identically distributed from a distribution from some known parametric family. This assumption may be suspect if either there is interaction between observed covariates and unobserved covariates or the fixed effects predictor of observed covariates is misspecified. Another cause for concern might be simply that the covariates affect more than just the location of the mixed effects distribution. As a consequence the distribution of the random effects could be highly irregular in modality and skewness leaving parametric families unable to model the distribution adequately. This paper therefore proposes a Bayesian nonparametric prior for the random effects to capture possible deviances in modality and skewness and to explore the observed covariates' effect on the distribution of the mixed effects.