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.     

Spatial–temporal variation of casuarina spread in Cauvery delta and north eastern zone of Tamil Nadu,India: a spatial autoregressive model

The low forest cover and productivity are the major obstacles for mitigating the demand supply gap of raw material for forest-based industries, which could be fulfilled from a tree outside forest area. Casuarina is a multi-utile, short rotation tree which adapts to all ecosystems. The casuarina wood is predominantly demanded for fuel, construction and paper industries which is mostly preferred by farmers, traders and industries. This study explores the spatial and temporal variability of casuarina spread in mitigating the gap of demand and supply in Tamil Nadu using a spatial autoregressive model. The spread of casuarina was spatially and temporally significant, which was negatively influenced by the gross area irrigated as main and direct effects and positively in an indirect effect. An assured irrigation forces the farmers to choose traditional agricultural crops for their livelihood in their own district. The increase in the price of casuarina would increase the spread of casuarina in both own district and neighbouring districts. The spread of casuarina would augment the supply of raw material for forest-based industries.     

Spatial measurement error in infectious disease models

Individual-level models (ILMs) for infectious disease can be used to model disease spread between individuals while taking into account important covariates. One important covariate in determining the risk of infection transfer can be spatial location. At the same time, measurement error is a concern in many areas of statistical analysis, and infectious disease modelling is no exception. In this paper, we are concerned with the issue of measurement error in the recorded location of individuals when using a simple spatial ILM to model the spread of disease within a population. An ILM that incorporates spatial location random effects is introduced within a hierarchical Bayesian framework. This model is tested upon both simulated data and data from the UK 2001 foot-and-mouth disease epidemic. The ability of the model to successfully identify both the spatial infection kernel and the basic reproduction number (R ₀) of the disease is tested.     

Generalized linear spatial models in epidemiology: A case study of zoonotic cutaneous leishmaniasis in Tunisia

Generalized linear spatial models (GLSM) are used here to study spatial characters of zoonotic cutaneous leishmaniasis (ZCL) in Tunisia. The response variable stands for the number of affected by district during the period 2001–2002. The model covariates are: climates (temperature and rainfall), humidity and surrounding vegetation status. As the environmental and weather data are not available for all the studied districts, Kriging based on linear interpolation was used to estimate the missing data. To account for unexplained spatial variation in the model, we include a stationary Gaussian process S with a powered exponential spatial correlation function. Moran coefficient, DIC criterion and residuals variograms are used to show the high goodness-of-fit of the GLSM. When compared with the statistical tools used in the previous ZCL studies, the optimal GLSM found here yields a better assessment of the impact of the risk factors, a better prediction of ZCL evolution and a better comprehension of the disease transmission. The statistical results show the progressive increase in the number of affected in zones with high temperature, low rainfall and high surrounding vegetation index. Relative humidity does not seem to affect the distribution of the disease in Tunisia. The results of the statistical analyses stress the important risk of misleading epidemiological conclusions when non-spatial models are used to analyse spatially structured data.     

Predicting infectious disease outbreak risk via migratory waterfowl vectors

The spread of an emerging infectious disease is a major public health threat. Given the uncertainties associated with vector-borne diseases, in terms of vector dynamics and disease transmission, it is critical to develop statistical models that address how and when such an infectious disease could spread throughout a region such as the USA. This paper considers a spatio-temporal statistical model for how an infectious disease could be carried into the USA by migratory waterfowl vectors during their seasonal migration and, ultimately, the risk of transmission of such a disease to domestic fowl. Modeling spatio-temporal data of this type is inherently difficult given the uncertainty associated with observations, complexity of the dynamics, high dimensionality of the underlying process, and the presence of excessive zeros. In particular, the spatio-temporal dynamics of the waterfowl migration are developed by way of a two-tiered functional temporal and spatial dimension reduction procedure that captures spatial and seasonal trends, as well as regional dynamics. Furthermore, the model relates the migration to a population of poultry farms that are known to be susceptible to such diseases, and is one of the possible avenues toward transmission to domestic poultry and humans. The result is a predictive distribution of those counties containing poultry farms that are at the greatest risk of having the infectious disease infiltrate their flocks assuming that the migratory population was infected. The model naturally fits into the hierarchical Bayesian framework.     

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.     

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     

The variability of rainfall acidity

Two years of rainfall acidity data for the eastern United States were analyzed. The data consist of rainfall-event pH measurements from a nine station monitoring network. A spatio-temporal stochastic model, including deterministic components for seasonal variation and rainfall washout, and stochastic components for spatial, temporal, and measurement variation, was fitted to the data. The fitted autocorrelation structure from this model was used, in the process known as Kriging, to obtain BLUE contour maps of seasonal and rainfall adjusted yearly average pH over the monitoring region.     

Statement of Withdrawal: Statistical analysis of an endemic disease from a capture–recapture experiment

There are a number of statistical techniques for analysing epidemic outbreaks. However, many diseases are endemic within populations and the analysis of such diseases are complicated by changing population demography. Motivated by the spread of cowpox among rodent populations, a combined mathematical model for population and disease dynamics is introduced. An MCMC algorithm is then constructed to make statistical inference for the model based on data being obtained from a capture–recapture experiment. The statistical analysis is used to identify the key elements in the spread of the cowpox virus.     

Statistical analysis of an endemic disease from a capture–recapture experiment

There are a number of statistical techniques for analysing epidemic outbreaks. However, many diseases are endemic within populations and the analysis of such diseases is complicated by changing population demography. Motivated by the spread of cowpox amongst rodent populations, a combined mathematical model for population and disease dynamics is introduced. A Markov chain Monte Carlo algorithm is then constructed to make statistical inference for the model based on data being obtained from a capture–recapture experiment. The statistical analysis is used to identify the key elements in the spread of the cowpox virus.     

On the clustering term in ecological analysis: how do different prior specifications affect results?

We study how different prior assumptions on the spatially structured heterogeneity term of the convolution hierarchical Bayesian model for spatial disease data could affect the results of an ecological analysis when response and exposure exhibit a strong spatial pattern. We show that in this case the estimate of the regression parameter could be strongly biased, both by analyzing the association between lung cancer mortality and education level on a real dataset and by a simulation experiment. The analysis is based on a hierarchical Bayesian model with a time dependent covariate in which we allow for a latency period between exposure and mortality, with time and space random terms and misaligned exposure-disease data.     

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.     

Dynamic models for spatiotemporal data

We propose a model for non-stationary spatiotemporal data. To account for spatial variability, we model the mean function at each time period as a locally weighted mixture of linear regressions. To incorporate temporal variation, we allow the regression coefficients to change through time. The model is cast in a Gaussian state space framework, which allows us to include temporal components such as trends, seasonal effects and autoregressions, and permits a fast implementation and full probabilistic inference for the parameters, interpolations and forecasts. To illustrate the model, we apply it to two large environmental data sets: tropical rainfall levels and Atlantic Ocean temperatures.     

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.     

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.     

Spatial–temporal model for wind speed in Lithuania

In this paper, we propose a spatial–temporal model for the wind speed (WS). We first estimate the model at the single spatial meteorological station independently on spatial correlations. The temporal model contains seasonality, a higher-order autoregressive component and a variance describing the remaining heteroskedesticity in residuals. We then model spatial dependencies by a Gaussian random field. The model is estimated on daily WS records from 18 meteorological stations in Lithuania. The validation procedure based on out-of-sample observations shows that the proposed model is reliable and can be used for various practical applications.     

A latent Gaussian Markov random-field model for spatiotemporal rainfall disaggregation

Summary. Rainfall data are often collected at coarser spatial scales than required for input into hydrology and agricultural models. We therefore describe a spatiotemporal model which allows multiple imputation of rainfall at fine spatial resolutions, with a realistic dependence structure in both space and time and with the total rainfall at the coarse scale consistent with that observed. The method involves the transformation of the fine scale rainfall to a thresholded Gaussian process which we model as a Gaussian Markov random field. Gibbs sampling is then used to generate realizations of rainfall efficiently at the fine scale. Results compare favourably with previous, less elegant methods.     

On Prediction for Correlated Domains in Longitudinal Surveys

In the survey sampling estimation or prediction of both population’s and subopulation’s (domain’s) characteristics is one of the key issues. In the case of the estimation or prediction of domain’s characteristics one of the problems is looking for additional sources of information that can be used to increase the accuracy of estimators or predictors. One of these sources may be spatial and temporal autocorrelation. Due to the mean squared error (MSE) estimation, the standard assumption is that random variables are independent for population elements from different domains. If the assumption is taken into account, spatial correlation may be assumed only inside domains. In the paper, we assume some special case of the linear mixed model with two random components that obey assumptions of the first-order spatial autoregressive model SAR(1) (but inside groups of domains instead of domains) and first-order temporal autoregressive model AR(1). Based on the model, the empirical best linear unbiased predictor will be proposed together with an estimator of its MSE taking the spatial correlation between domains into account.     

Optimal design of air quality networks detecting warning and alert conditions

A statistical method is presented to determine the optima design of air quality networks detecting warning and alert levels. A simulation model is used to describe temporal and spatial variations of atmospheric pollutants; air quality patterns serve as the database of the procedure to design the network. Only the sites exceeding warning and alert levels, at different meteorological scenarios, are considered as potential monitoring stations. For the selection of the optima set, spatial and temporal representativity criteria are introduced; accordingly, the optima set provides a complete representativity of the space and time considered. The method is applied to the Mestre urban area, in Venice district, for the carbon monoxide pollutant.     

A hierarchical model for space–time surveillance data on meningococcal disease incidence

Summary. We describe a model-based approach to analyse space–time surveillance data on meningococcal disease. Such data typically comprise a number of time series of disease counts, each representing a specific geographical area. We propose a hierarchical formulation, where latent parameters capture temporal, seasonal and spatial trends in disease incidence. We then add—for each area—a hidden Markov model to describe potential additional (autoregressive) effects of the number of cases at the previous time point. Different specifications for the functional form of this autoregressive term are compared which involve the number of cases in the same or in neighbouring areas. The two states of the Markov chain can be interpreted as representing an 'endemic' and a 'hyperendemic' state. The methodology is applied to a data set of monthly counts of the incidence of meningococcal disease in the 94 départements of France from 1985 to 1997. Inference is carried out by using Markov chain Monte Carlo simulation techniques in a fully Bayesian framework. We emphasize that a central feature of our model is the possibility of calculating—for each region and each time point—the posterior probability of being in a hyperendemic state, adjusted for global spatial and temporal trends, which we believe is of particular public health interest.