Comparison of three-dimensional profiles over time

In this paper, we describe an analysis for data collected on a three-dimensional spatial lattice with treatments applied at the horizontal lattice points. Spatial correlation is accounted for using a conditional autoregressive model. Observations are defined as neighbours only if they are at the same depth. This allows the corresponding variance components to vary by depth. We use the Markov chain Monte Carlo method with block updating, together with Krylov subspace methods, for efficient estimation of the model. The method is applicable to both regular and irregular horizontal lattices and hence to data collected at any set of horizontal sites for a set of depths or heights, for example, water column or soil profile data. The model for the three-dimensional data is applied to agricultural trial data for five separate days taken roughly six months apart in order to determine possible relationships over time. The purpose of the trial is to determine a form of cropping that leads to less moist soils in the root zone and beyond. We estimate moisture for each date, depth and treatment accounting for spatial correlation and determine relationships of these and other parameters over time.     

BAYESIAN HIDDEN MARKOV MODELS FOR LONGITUDINAL COUNTS

This paper describes a Bayesian approach to modelling carcinogenity in animal studies where the data consist of counts of the number of tumours present over time. It compares two autoregressive hidden Markov models. One of them models the transitions between three latent states: an inactive transient state, a multiplying state for increasing counts and a reducing state for decreasing counts. The second model introduces a fourth tied state to describe non‐zero observations that are neither increasing nor decreasing. Both these models can model the length of stay upon entry of a state. A discrete constant hazards waiting time distribution is used to model the time to onset of tumour growth. Our models describe between‐animal‐variability by a single hierarchy of random effects and the within‐animal variation by first‐order serial dependence. They can be extended to higher‐order serial dependence and multi‐level hierarchies. Analysis of data from animal experiments comparing the influence of two genes leads to conclusions that differ from those of Dunson (2000). The observed data likelihood defines an information criterion to assess the predictive properties of the three‐ and four‐state models. The deviance information criterion is appropriately defined for discrete parameters.     

Best subset selection of autoregressive models with exogenous variables and generalized autoregressive conditional heteroscedasticity errors

Summary.  We develop an efficient way to select the best subset autoregressive model with exogenous variables and generalized autoregressive conditional heteroscedasticity errors. One main feature of our method is to select important autoregressive and exogenous variables, and at the same time to estimate the unknown parameters. The method proposed uses the stochastic search idea. By adopting Markov chain Monte Carlo techniques, we can identify the best subset model from a large of number of possible choices. A simulation experiment shows that the method is very effective. Misspecification in the mean equation can also be detected by our model selection method. In the application to the stock-market data of seven countries, the lagged 1 US return is found to have a strong influence on the other stock-market returns.     

Longitudinal network models and permutation-uniform Markov chains

Consider longitudinal networks whose edges turn on and off according to a discrete-time Markov chain with exponential-family transition probabilities. We characterize when their joint distributions are also exponential families with the same parameter, improving data reduction. Further we show that the permutation-uniform subclass of these chains permit interpretation as an independent, identically distributed sequence on the same state space. We then apply these ideas to temporal exponential random graph models, for which permutation uniformity is well suited, and discuss mean-parameter convergence, dyadic independence, and exchangeability. Our framework facilitates our introducing a new network model; simplifies analysis of some network and autoregressive models from the literature, including by permitting closed-form expressions for maximum likelihood estimates for some models; and facilitates applying standard tools to longitudinal-network Markov chains from either asymptotics or single-observation exponential random graph models.     

Venezuelan Rainfall Data Analysed by Using a Bayesian Space–time Model

We consider a set of data from 80 stations in the Venezuelan state of Guárico consisting of accumulated monthly rainfall in a time span of 16 years. The problem of modelling rainfall accumulated over fixed periods of time and recorded at meteorological stations at different sites is studied by using a model based on the assumption that the data follow a truncated and transformed multivariate normal distribution. The spatial correlation is modelled by using an exponentially decreasing correlation function and an interpolating surface for the means. Missing data and dry periods are handled within a Markov chain Monte Carlo framework using latent variables. We estimate the amount of rainfall as well as the probability of a dry period by using the predictive density of the data. We considered a model based on a full second-degree polynomial over the spatial co-ordinates as well as the first two Fourier harmonics to describe the variability during the year. Predictive inferences on the data show very realistic results, capturing the typical rainfall variability in time and space for that region. Important extensions of the model are also discussed.     

Markov Chain Monte Carlo Methods for Fitting Spatiotemporal Stochastic Models in Plant Epidemiology

Strategies for controlling plant epidemics are investigated by fitting continuous time spatiotemporal stochastic models to data consisting of maps of disease incidence observed at discrete times. Markov chain Monte Carlo methods are used for fitting two such models to data describing the spread of citrus tristeza virus (CTV) in an orchard. The approach overcomes some of the difficulties encountered when fitting stochastic models to infrequent observations of a continuous process. The results of the analysis cast doubt on the effectiveness of a strategy identified from a previous spatial analysis of the CTV data. Extensions of the approaches to more general models and other problems are also considered.     

Hierarchical Bayesian bivariate disease mapping: analysis of children and adults asthma visits to hospital

In spatial epidemiology, detecting areas with high ratio of disease is important as it may lead to identifying risk factors associated with disease. This in turn may lead to further epidemiological investigations into the nature of disease. Disease mapping studies have been widely performed with considering only one disease in the estimated models. Simultaneous modelling of different diseases can also be a valuable tool both from the epidemiological and also from the statistical point of view. In particular, when we have several measurements recorded at each spatial location, one can consider multivariate models in order to handle the dependence among the multivariate components and the spatial dependence between locations. In this paper, spatial models that use multivariate conditionally autoregressive smoothing across the spatial dimension are considered. We study the patterns of incidence ratios and identify areas with consistently high ratio estimates as areas for further investigation. A hierarchical Bayesian approach using Markov chain Monte Carlo techniques is employed to simultaneously examine spatial trends of asthma visits by children and adults to hospital in the province of Manitoba, Canada, during 2000–2010.     

A grouped beta process model for multivariate resting‐state EEG microstate analysis on twins

EEG microstate analysis investigates the collection of distinct temporal blocks that characterize the electrical activity of the brain. Brain activity within each microstate is stable, but activity switches rapidly between different microstates in a nonrandom way. We propose a Bayesian nonparametric model that concurrently estimates the number of microstates and their underlying behaviour. We use a Markov switching vector autoregressive (VAR) framework, where a hidden Markov model (HMM) controls the nonrandom state switching dynamics of the EEG activity and a VAR model defines the behaviour of all time points within a given state. We analyze the resting‐state EEG data from twin pairs collected through the Minnesota Twin Family Study, consisting of 70 epochs per participant, where each epoch corresponds to 2 s of EEG data. We fit our model at the twin pair level, sharing information within epochs from the same participant and within epochs from the same twin pair. We capture within twin‐pair similarity, using an Indian buffet process, to consider an infinite library of microstates, allowing each participant to select a finite number of states from this library. The state spaces of highly similar twins may completely overlap while dissimilar twins could select distinct state spaces. In this way, our Bayesian nonparametric model defines a sparse set of states that describe the EEG data. All epochs from a single participant use the same set of states and are assumed to adhere to the same state switching dynamics in the HMM model, enforcing within‐participant similarity.     

Modelling spatially correlated data via mixtures: a Bayesian approach

Summary. The paper develops mixture models for spatially indexed data. We confine attention to the case of finite, typically irregular, patterns of points or regions with prescribed spatial relationships, and to problems where it is only the weights in the mixture that vary from one location to another. Our specific focus is on Poisson-distributed data, and applications in disease mapping. We work in a Bayesian framework, with the Poisson parameters drawn from gamma priors, and an unknown number of components. We propose two alternative models for spatially dependent weights, based on transformations of autoregressive Gaussian processes: in one (the logistic normal model), the mixture component labels are exchangeable; in the other (the grouped continuous model), they are ordered. Reversible jump Markov chain Monte Carlo algorithms for posterior inference are developed. Finally, the performances of both of these formulations are examined on synthetic data and real data on mortality from a rare disease.     

Bayesian analysis of multivariate threshold autoregressive models with missing data

In some fields, we are forced to work with missing data in multivariate time series. Unfortunately, the data analysis in this context cannot be carried out in the same way as in the case of complete data. To deal with this problem, a Bayesian analysis of multivariate threshold autoregressive models with exogenous inputs and missing data is carried out. In this paper, Markov chain Monte Carlo methods are used to obtain samples from the involved posterior distributions, including threshold values and missing data. In order to identify autoregressive orders, we adapt the Bayesian variable selection method in this class of multivariate process. The number of regimes is estimated using marginal likelihood or product parameter-space strategies.     

A shared component model for detecting joint and selective clustering of two diseases

The study of spatial variations in disease rates is a common epidemiological approach used to describe the geographical clustering of diseases and to generate hypotheses about the possible 'causes' which could explain apparent differences in risk. Recent statistical and computational developments have led to the use of realistically complex models to account for overdispersion and spatial correlation. However, these developments have focused almost exclusively on spatial modelling of a single disease. Many diseases share common risk factors (smoking being an obvious example) and, if similar patterns of geographical variation of related diseases can be identified, this may provide more convincing evidence of real clustering in the underlying risk surface. We propose a shared component model for the joint spatial analysis of two diseases. The key idea is to separate the underlying risk surface for each disease into a shared and a disease-specific component. The various components of this formulation are modelled simultaneously by using spatial cluster models implemented via reversible jump Markov chain Monte Carlo methods. We illustrate the methodology through an analysis of oral and oesophageal cancer mortality in the 544 districts of Germany, 1986–1990.     

Uniform Ergodicity of the Particle Gibbs Sampler

The particle Gibbs sampler is a systematic way of using a particle filter within Markov chain Monte Carlo. This results in an off‐the‐shelf Markov kernel on the space of state trajectories, which can be used to simulate from the full joint smoothing distribution for a state space model in a Markov chain Monte Carlo scheme. We show that the particle Gibbs Markov kernel is uniformly ergodic under rather general assumptions, which we will carefully review and discuss. In particular, we provide an explicit rate of convergence, which reveals that (i) for fixed number of data points, the convergence rate can be made arbitrarily good by increasing the number of particles and (ii) under general mixing assumptions, the convergence rate can be kept constant by increasing the number of particles superlinearly with the number of observations. We illustrate the applicability of our result by studying in detail a common stochastic volatility model with a non‐compact state space.     

Markov switching model of nonlinear autoregressive with skew-symmetric innovations

We consider data generating structures which can be represented as a Markov switching of nonlinear autoregressive model with considering skew-symmetric innovations such that switching between the states is controlled by a hidden Markov chain. We propose semi-parametric estimators for the nonlinear functions of the proposed model based on a maximum likelihood (ML) approach and study sufficient conditions for geometric ergodicity of the process. Also, an Expectation-Maximization type optimization for obtaining the ML estimators are presented. A simulation study and a real world application are also performed to illustrate and evaluate the proposed methodology.     

Adaptive Gaussian Markov random fields with applications in human brain mapping

Summary.  Functional magnetic resonance imaging has become a standard technology in human brain mapping. Analyses of the massive spatiotemporal functional magnetic resonance imaging data sets often focus on parametric or non-parametric modelling of the temporal component, whereas spatial smoothing is based on Gaussian kernels or random fields. A weakness of Gaussian spatial smoothing is underestimation of activation peaks or blurring of high curvature transitions between activated and non-activated regions of the brain. To improve spatial adaptivity, we introduce a class of inhomogeneous Markov random fields with stochastic interaction weights in a space-varying coefficient model. For given weights, the random field is conditionally Gaussian, but marginally it is non-Gaussian. Fully Bayesian inference, including estimation of weights and variance parameters, can be carried out through efficient Markov chain Monte Carlo simulation. Although motivated by the analysis of functional magnetic resonance imaging data, the methodological development is general and can also be used for spatial smoothing and regression analysis of areal data on irregular lattices. An application to stylized artificial data and to real functional magnetic resonance imaging data from a visual stimulation experiment demonstrates the performance of our approach in comparison with Gaussian and robustified non-Gaussian Markov random-field models.     

Parallel discretization of the Markov chain approximation for the autoregressive moving average chart

Abstract

In the Markov chain model of an autoregressive moving average chart, the post-transition states of nonzero transition probabilities are distributed along one-dimensional lines of a constant gradient over the state space. By considering this characteristic, we propose discretizing the state space parallel to the gradient of these one-dimensional lines. We demonstrate that our method substantially reduces the computational cost of the Markov chain approximation for the average run length in two- and three-dimensional state spaces. Also, we investigate the effect of these one-dimensional lines on the computational cost. Lastly, we generalize our method to state spaces larger than three dimensions.     

Spatio-temporal modeling of infectious disease dynamics

A stochastic model, which is well suited to capture space–time dependence of an infectious disease, was employed in this study to describe the underlying spatial and temporal pattern of measles in Barisal Division, Bangladesh. The model has two components: an endemic component and an epidemic component; weights are used in the epidemic component for better accounting of the disease spread into different geographical regions. We illustrate our findings using a data set of monthly measles counts in the six districts of Barisal, from January 2000 to August 2009, collected from the Expanded Program on Immunization, Bangladesh. The negative binomial model with both the seasonal and autoregressive components was found to be suitable for capturing space–time dependence of measles in Barisal. Analyses were done using general optimization routines, which provided the maximum likelihood estimates with the corresponding standard errors.     

A joint modeling approach for spatial earthquake risk variations

Modeling spatial patterns and processes to assess the spatial variations of data over a study region is an important issue in many fields. In this paper, we focus on investigating the spatial variations of earthquake risks after a main shock. Although earthquake risks have been extensively studied in the literatures, to our knowledge, there does not exist a suitable spatial model for assessing the problem. Therefore, we propose a joint modeling approach based on spatial hierarchical Bayesian models and spatial conditional autoregressive models to describe the spatial variations in earthquake risks over the study region during two periods. A family of stochastic algorithms based on a Markov chain Monte Carlo technique is then performed for posterior computations. The probabilistic issue for the changes of earthquake risks after a main shock is also discussed. Finally, the proposed method is applied to the earthquake records for Taiwan before and after the Chi-Chi earthquake.     

Transient analysis of a finite source discrete-time queueing system using homogeneous Markov system with state size capacities (HMS/c)

Abstract

In this article, a finite source discrete-time queueing system is modeled as a discrete-time homogeneous Markov system with finite state size capacities (HMS/c) and transition priorities. This Markov system is comprised of three states. The first state of the HMS/c corresponds to the source and the second one to the state with the servers. The second state has a finite capacity which corresponds to the number of servers. The members of the system which can not enter the second state, due to its finite capacity, enter the third state which represents the system's queue. In order to examine the variability of the state sizes recursive formulae for their factorial and mixed factorial moments are derived in matrix form. As a consequence the probability mass function of each state size can be evaluated. Also the expected time in queue is computed by means of the interval transition probabilities. The theoretical results are illustrated by a numerical example.     

Semiparametric latent variable regression models for spatiotemporal modelling of mobile source particles in the greater Boston area

Summary.  Traffic particle concentrations show considerable spatial variability within a metropolitan area. We consider latent variable semiparametric regression models for modelling the spatial and temporal variability of black carbon and elemental carbon concentrations in the greater Boston area. Measurements of these pollutants, which are markers of traffic particles, were obtained from several individual exposure studies that were conducted at specific household locations as well as 15 ambient monitoring sites in the area. The models allow for both flexible non-linear effects of covariates and for unexplained spatial and temporal variability in exposure. In addition, the different individual exposure studies recorded different surrogates of traffic particles, with some recording only outdoor concentrations of black or elemental carbon, some recording indoor concentrations of black carbon and others recording both indoor and outdoor concentrations of black carbon. A joint model for outdoor and indoor exposure that specifies a spatially varying latent variable provides greater spatial coverage in the area of interest. We propose a penalized spline formulation of the model that relates to generalized kriging of the latent traffic pollution variable and leads to a natural Bayesian Markov chain Monte Carlo algorithm for model fitting. We propose methods that allow us to control the degrees of freedom of the smoother in a Bayesian framework. Finally, we present results from an analysis that applies the model to data from summer and winter separately.     

Modelling count data with overdispersion and spatial effects

In this paper we consider regression models for count data allowing for overdispersion in a Bayesian framework. We account for unobserved heterogeneity in the data in two ways. On the one hand, we consider more flexible models than a common Poisson model allowing for overdispersion in different ways. In particular, the negative binomial and the generalized Poisson (GP) distribution are addressed where overdispersion is modelled by an additional model parameter. Further, zero-inflated models in which overdispersion is assumed to be caused by an excessive number of zeros are discussed. On the other hand, extra spatial variability in the data is taken into account by adding correlated spatial random effects to the models. This approach allows for an underlying spatial dependency structure which is modelled using a conditional autoregressive prior based on Pettitt et al. in Stat Comput 12(4):353–367, (2002). In an application the presented models are used to analyse the number of invasive meningococcal disease cases in Germany in the year 2004. Models are compared according to the deviance information criterion (DIC) suggested by Spiegelhalter et al. in J R Stat Soc B64(4):583–640, (2002) and using proper scoring rules, see for example Gneiting and Raftery in Technical Report no. 463, University of Washington, (2004). We observe a rather high degree of overdispersion in the data which is captured best by the GP model when spatial effects are neglected. While the addition of spatial effects to the models allowing for overdispersion gives no or only little improvement, spatial Poisson models with spatially correlated or uncorrelated random effects are to be preferred over all other models according to the considered criteria.