A Bayesian hierarchical spatio-temporal rainfall model

A Bayesian hierarchical spatio-temporal rainfall model is presented and analysed. The model has the ability to deal with extensive missing or null values, uses a sophisticated variance stabilising rainfall pre-transformation, incorporates a new elevation model and can provide sub-catchment rainfall estimation and interpolation using a sequential kriging scheme. The model uses a vector autoregressive stochastic process to represent the time dependence of the rainfall field and an exponential covariogram to model the spatial correlation of the rainfall field. The model can be readily generalised to other types of stochastic processes. In this paper, some results of applying the model to a particular rainfall catchment are presented.     

A prior for the variance in hierarchical models

The choice of prior distributions for the variances can be important and quite difficult in Bayesian hierarchical and variance component models. For situations where little prior information is available, a ‘nonin-formative’ type prior is usually chosen. ‘Noninformative’ priors have been discussed by many authors and used in many contexts. However, care must be taken using these prior distributions as many are improper and thus, can lead to improper posterior distributions. Additionally, in small samples, these priors can be ‘informative’. In this paper, we investigate a proper ‘vague’ prior, the uniform shrinkage prior (Strawder-man 1971; Christiansen & Morris 1997). We discuss its properties and show how posterior distributions for common hierarchical models using this prior lead to proper posterior distributions. We also illustrate the attractive frequentist properties of this prior for a normal hierarchical model including testing and estimation. To conclude, we generalize this prior to the multivariate situation of a covariance matrix.     

Regression spline bivariate probit models: A practical approach to testing for exogeneity

Bivariate probit models can deal with a problem usually known as endogeneity. This issue is likely to arise in observational studies when confounders are unobserved. We are concerned with testing the hypothesis of exogeneity (or absence of endogeneity) when using regression spline recursive and sample selection bivariate probit models. Likelihood ratio and gradient tests are discussed in this context and their empirical properties investigated and compared with those of the Lagrange multiplier and Wald tests through a Monte Carlo study. The tests are illustrated using two datasets in which the hypothesis of exogeneity needs to be tested.     

A spatio-temporal model for assessing winter damage risk to east coast vineyards

Climate is an essential component in site suitability for agriculture in general, and specifically in viticulture. With the recent increase in vineyards on the East Coast, an important climactic consideration in site suitability is extreme winter temperature. Often, maps of annual minimum temperatures are used to determine cold hardiness. However, cold hardiness of grapes is a more complicated process, since the temperature that grapes are able to withstand without damage is not constant. Rather, recent temperature cause acclimation or deacclimation and hence, have a large influence on cold hardiness. By combining National Oceanic and Atmospheric Administration (NOAA) weather station data and leveraging recently created cold hardiness models for grapes, we develop a dynamic spatio-temporal model to determine the risk of winter damage due to extreme cold for several grape varieties commonly grown in the eastern United States. This analysis provides maps of winter damage risk to three grape varieties, Chardonnay, Cabernet Sauvignon, and Concord.     

Bayesian hierarchical models for linear networks

The purpose of this study is to highlight dangerous motorways via estimating the intensity of accidents and study its pattern across the UK motorway network. Two methods have been developed to achieve this aim. First, the motorway-specific intensity is estimated by using a homogeneous Poisson process. The heterogeneity across motorways is incorporated using two-level hierarchical models. The data structure is multilevel since each motorway consists of junctions that are joined by grouped segments. In the second method, the segment-specific intensity is estimated. The homogeneous Poisson process is used to model accident data within grouped segments but heterogeneity across grouped segments is incorporated using three-level hierarchical models. A Bayesian method via Markov Chain Monte Carlo is used to estimate the unknown parameters in the models and the sensitivity to the choice of priors is assessed. The performance of the proposed models is evaluated by a simulation study and an application to traffic accidents in 2016 on the UK motorway network. The deviance information criterion (DIC) and the widely applicable information criterion (WAIC) are employed to choose between models.     

Inference for multivariate normal hierarchical models

This paper provides a new method and algorithm for making inferences about the parameters of a two-level multivariate normal hierarchical model. One has observed J p -dimensional vector outcomes, distributed at level 1 as multivariate normal with unknown mean vectors and with known covariance matrices. At level 2, the unknown mean vectors also have normal distributions, with common unknown covariance matrix A and with means depending on known covariates and on unknown regression coefficients. The algorithm samples independently from the marginal posterior distribution of A by using rejection procedures. Functions such as posterior means and covariances of the level 1 mean vectors and of the level 2 regression coefficient are estimated by averaging over posterior values calculated conditionally on each value of A drawn. This estimation accounts for the uncertainty in A , unlike standard restricted maximum likelihood empirical Bayes procedures. It is based on independent draws from the exact posterior distributions, unlike Gibbs sampling. The procedure is demonstrated for profiling hospitals based on patients' responses concerning p =2 types of problems (non-surgical and surgical). The frequency operating characteristics of the rule corresponding to a particular vague multivariate prior distribution are shown via simulation to achieve their nominal values in that setting.     

Bayesian hierarchical models for the prediction of volleyball results

Statistical modelling of sports data has become more and more popular in the recent years and different types of models have been proposed to achieve a variety of objectives: from identifying the key characteristics which lead a team to win or lose to predicting the outcome of a game or the team rankings in national leagues. Although not as popular as football or basketball, volleyball is a team sport with both national and international level competitions in almost every country. However, there is almost no study investigating the prediction of volleyball game outcomes and team rankings in national leagues. We propose a Bayesian hierarchical model for the prediction of the rankings of volleyball national teams, which also allows to estimate the results of each match in the league. We consider two alternative model specifications of different complexity which are validated using data from the women''s volleyball Italian Serie A1 2017–2018 season.     

Estimating likelihoods for spatio-temporal models using importance sampling

This paper describes how importance sampling can be applied to estimate likelihoods for spatio-temporal stochastic models of epidemics in plant populations, where observations consist of the set of diseased individuals at two or more distinct times. Likelihood computation is problematic because of the inherent lack of independence of the status of individuals in the population whenever disease transmission is distance-dependent. The methods of this paper overcome this by partitioning the population into a number of sectors and then attempting to take account of this dependence within each sector, while neglecting that between-sectors. Application to both simulated and real epidemic data sets show that the techniques perform well in comparison with existing approaches. Moreover, the results confirm the validity of likelihood estimates obtained elsewhere using Markov chain Monte Carlo methods.     

Estimation of parameterized spatio-temporal dynamic models

Spatio-temporal processes are often high-dimensional, exhibiting complicated variability across space and time. Traditional state-space model approaches to such processes in the presence of uncertain data have been shown to be useful. However, estimation of state-space models in this context is often problematic since parameter vectors and matrices are of high dimension and can have complicated dependence structures. We propose a spatio-temporal dynamic model formulation with parameter matrices restricted based on prior scientific knowledge and/or common spatial models. Estimation is carried out via the expectation–maximization (EM) algorithm or general EM algorithm. Several parameterization strategies are proposed and analytical or computational closed form EM update equations are derived for each. We apply the methodology to a model based on an advection–diffusion partial differential equation in a simulation study and also to a dimension-reduced model for a Palmer Drought Severity Index (PDSI) data set.     

Bayesian quantile regression for hierarchical linear models

The paper proposes a Bayesian quantile regression method for hierarchical linear models. Existing approaches of hierarchical linear quantile regression models are scarce and most of them were not from the perspective of Bayesian thoughts, which is important for hierarchical models. In this paper, based on Bayesian theories and Markov Chain Monte Carlo methods, we introduce Asymmetric Laplace distributed errors to simulate joint posterior distributions of population parameters and across-unit parameters and then derive their posterior quantile inferences. We run a simulation as the proposed method to examine the effects on parameters induced by units and quantile levels; the method is also applied to study the relationship between Chinese rural residents' family annual income and their cultivated areas. Both the simulation and real data analysis indicate that the method is effective and accurate.     

Bayesian hierarchical models for food frequency assessment

The aim of this study is to assess the biases of a Food Frequency Questionnaire (FFQ) by comparing total energy intake (TEI) with total energy expenditure (TEE) obtained from doubly labelled water(DLW) biomarker after adjusting measurement errors in DLW. We develop several Bayesian hierarchical measurement error models of DLW with different distributional assumptions on TEI to obtain precise bias estimates of TEI. Inference is carried out by using MCMC simulation techniques in a fully Bayesian framework, and model comparisons are done via the mean square predictive error. Our results showed that the joint model with random effects under the Gamma distribution is the best fit model in terms of the MSPE and residual diagnostics, in which bias in TEI is not significant based on the 95% credible interval. The Canadian Journal of Statistics 38: 506–516; 2010 © 2010 Statistical Society of Canada     

A practical extension of the generalized estimating equation approach for longitudinal data

Liang and Zeger (1986) proposed an extension of generalized linear models to the analysis of longitudinal data. In their formulation, a common dispersion parameter assumption across observation times is required. However, this assumption is not expected to hold in most situations. Park (1993) proposed a simple extension of Liang and Zeger's formulation to allow for different dispersion parameters for each time point. The proposed model is easy to apply without heavy computations and useful to handle the cases when variations in over-dispersion over time exist. In this paper, we focus on evaluating the effect of additional dispersion parameters on the estimators of model parameters. Through a Monte Carlo simulation study, efficiency of Park's method is compared with the Liang and Zeger's method.     

Marginal models for the association structure of hierarchical binary responses

Clustered binary responses are often found in ecological studies. Data analysis may include modeling the marginal probability response. However, when the association is the main scientific focus, modeling the correlation structure between pairs of responses is the key part of the analysis. Second-order generalized estimating equations (GEE) are established in the literature. Some of them are more efficient in computational terms, especially facing large clusters. Alternating logistic regression (ALR) and orthogonalized residual (ORTH) GEE methods are presented and compared in this paper. Simulation results show a slightly superiority of ALR over ORTH. Marginal probabilities and odds ratios are also estimated and compared in a real ecological study involving a three-level hierarchical clustering. ALR and ORTH models are useful for modeling complex association structure with large cluster sizes.     

Genetic algorithms for the analysis of Bayesian hierarchical partition models

Hierarchical partition models (see Malec and Sedransk, 1992, Consonni and Veronese, 1995) aim at finding an optimal grouping (partition) of a set of experiments regarding a target variable. In this class of models the partition is regarded as an unknown parameter, and one of the main goals is computing the posterior distribution over the class of the possible partitions. This problem has been addressed in Sampietro and Veronese (1998), where a Metropolis-Hastings algorithm is applied. In this paper the performance of an alternative procedure, based on the logic of genetic algorithms, is evaluated. The results of the two approaches are compared, even if a conjoint use of them is to be advised.     

Simplified hierarchical linear models for the evaluation of surrogate endpoints

The linear mixed-effects model (Verbeke and Molenberghs, 2000) has become a standard tool for the analysis of continuous hierarchical data such as, for example, repeated measures or data from meta-analyses. However, in certain situations the model does pose insurmountable computational problems. Precisely this has been the experience of Buyse et al. (2000a) who proposed an estimation- and prediction-based approach for evaluating surrogate endpoints. Their approach requires fitting linear mixed models to data from several clinical trials. In doing so, these authors built on the earlier, single-trial based, work by Prentice (1989), Freedman et al. (1992), and Buyse and Molenberghs (1998). While Buyse et al. (2000a) claim their approach has a number of advantages over the classical single-trial methods, a solution needs to be found for the computational complexity of the corresponding linear mixed model. In this paper, we propose and study a number of possible simplifications. This is done by means of a simulation study and by applying the various strategies to data from three clinical studies: Pharmacological Therapy for Macular Degeneration Study Group (1977), Ovarian Cancer Meta-analysis Project (1991) and Corfu-A Study Group (1995).     

Conservative prior distributions for variance parameters in hierarchical models

Bayesian hierarchical models typically involve specifying prior distributions for one or more variance components. This is rather removed from the observed data, so specification based on expert knowledge can be difficult. While there are suggestions for “default” priors in the literature, often a conditionally conjugate inverse‐gamma specification is used, despite documented drawbacks of this choice. The authors suggest “conservative” prior distributions for variance components, which deliberately give more weight to smaller values. These are appropriate for investigators who are skeptical about the presence of variability in the second‐stage parameters (random effects) and want to particularly guard against inferring more structure than is really present. The suggested priors readily adapt to various hierarchical modelling settings, such as fitting smooth curves, modelling spatial variation and combining data from multiple sites.     

A hierarchical approach to the study of the exponential failure model

The exponential failure model is studied from the hierarchical point of view. The parameter of the exponential is considered as a random variable with a gamma function as a prior. Futhermore, the scale parameter of the gamma prior isassumed to be a random variable with known hyperprior. Under these assumptions estimators are derived for the exponential parameter and reliability function. Monte Carlo simulation is utilized to compare the various estimators.     

Stochastic models for greenhouse gas emission rate estimation from hydroelectric reservoirs: a Bayesian hierarchical approach

Herein, we propose a fully Bayesian approach to the greenhouse gas emission problem. The goal of this work is to estimate the emission rate of polluting gases from the area flooded by hydroelectric reservoirs. We present models for gas concentration evolution in two ways: first, by proposing them from ordinary differential equation solutions and, second, by using stochastic differential equations with a discretization scheme. Finally, we present techniques to estimate the emission rate for the entire reservoir. In order to carry out the inference, we use the Bayesian framework with Monte Carlo via Markov Chain methods. Discretization schemes over continuous differential equations are used when necessary. These models applied to greenhouse gas emission and Bayesian inference for this purpose are completely new in statistical literature, as far as we know, and contribute to estimate the amount of polluting gases released from hydroelectric reservoirs in Brazil. The proposed models are applied in a real data set and results are presented.     

Triple-goal estimates in two-stage hierarchical models

The beauty of the Bayesian approach is its ability to structure complicated models, inferential goals and analyses. To take full advantage of it, methods should be linked to an inferential goal via a loss function. For example, in the two-stage, compound sampling model the posterior means are optimal under squared error loss. However, they can perform poorly in estimating the histogram of the parameters or in ranking them. 'Triple-goal' estimates are motivated by the desire to have a set of estimates that produce good ranks, a good parameter histogram and good co-ordinate-specific estimates. No set of estimates can simultaneously optimize these three goals and we seek a set that strikes an effective trade-off. We evaluate and compare three candidate approaches: the posterior means, the constrained Bayes estimates of Louis and Ghosh, and a new approach that optimizes estimation of the histogram and the ranks. Mathematical and simulation-based analyses support the superiority of the new approach and document its excellent performance for the three inferential goals.