Spatial modelling for binary data using␣a␣hidden conditional autoregressive Gaussian process: a multivariate extension of the probit model

A Bayesian approach to modelling binary data on a regular lattice is introduced. The method uses a hierarchical model where the observed data is the sign of a hidden conditional autoregressive Gaussian process. This approach essentially extends the familiar probit model to dependent data. Markov chain Monte Carlo simulations are used on real and simulated data to estimate the posterior distribution of the spatial dependency parameters and the method is shown to work well. The method can be straightforwardly extended to regression models.     

A model for analyzing spatially correlated binary data clustered in uncorrelated lattices

In recent years, the spatial lattice data has been a motivating issue for researches. Modeling of binary variables observed at locations on a spatial lattice has been sufficiently investigated and the autologistic model is a popular tool for analyzing these data. But, there are many situations where binary responses are clustered in several uncorrelated lattices, and only a few studies were found to investigate the modeling of binary data distributed in such spatial structure. Besides, due to spatial dependency in data exact likelihood analyses is not possible. Bayesian inference, for the autologistic function due to intractability of its normalizing-constant, often has limitations and difficulties. In this study, spatially correlated binary data clustered in uncorrelated lattices are modeled via autologistic regression and IBF (inverse Bayes formulas) sampler with help of introducing latent variables, is extended for posterior analysis and parameter estimation. The proposed methodology is illustrated using simulated and real observations.     

Sample-based Maximum Likelihood Estimation of the Autologistic Model

New recursive algorithms for fast computation of the normalizing constant for the autologistic model on the lattice make feasible a sample-based maximum likelihood estimation (MLE) of the autologistic parameters. We demonstrate by sampling from 12 simulated 420×420 binary lattices with square lattice plots of size 4×4, …, 7×7 and sample sizes between 20 and 600. Sample-based results are compared with ‘benchmark’ MCMC estimates derived from all binary observations on a lattice. Sample-based estimates are, on average, biased systematically by 3%–7%, a bias that can be reduced by more than half by a set of calibrating equations. MLE estimates of sampling variances are large and usually conservative. The variance of the parameter of spatial association is about 2–10 times higher than the variance of the parameter of abundance. Sample distributions of estimates were mostly non-normal. We conclude that sample-based MLE estimation of the autologistic parameters with an appropriate sample size and post-estimation calibration will furnish fully acceptable estimates. Equations for predicting the expected sampling variance are given.     

Efficient calculation of the normalizing constant of the autologistic and related models on the cylinder and lattice

Summary. Motivated by the autologistic model for the analysis of spatial binary data on the two-dimensional lattice, we develop efficient computational methods for calculating the normalizing constant for models for discrete data defined on the cylinder and lattice. Because the normalizing constant is generally unknown analytically, statisticians have developed various ad hoc methods to overcome this difficulty. Our aim is to provide computationally and statistically efficient methods for calculating the normalizing constant so that efficient likelihood-based statistical methods are then available for inference. We extend the so-called transition method to find a feasible computational method of obtaining the normalizing constant for the cylinder boundary condition. To extend the result to the free-boundary condition on the lattice we use an efficient path sampling Markov chain Monte Carlo scheme. The methods are generally applicable to association patterns other than spatial, such as clustered binary data, and to variables taking three or more values described by, for example, Potts models.     

Analysis of clustered spatially correlated binary data using autologistic model and Bayesian method with an application to dental caries of 3–5-year-old children

The autologistic model, first introduced by Besag, is a popular tool for analyzing binary data in spatial lattices. However, no investigation was found to consider modeling of binary data clustered in uncorrelated lattices. Owing to spatial dependency of responses, the exact likelihood estimation of parameters is not possible. For circumventing this difficulty, many studies have been designed to approximate the likelihood and the related partition function of the model. So, the traditional and Bayesian estimation methods based on the likelihood function are often time-consuming and require heavy computations and recursive techniques. Some investigators have introduced and implemented data augmentation and latent variable model to reduce computational complications in parameter estimation. In this work, the spatially correlated binary data distributed in uncorrelated lattices were modeled using autologistic regression, a Bayesian inference was developed with contribution of data augmentation and the proposed models were applied to caries experiences of deciduous dents.     

A Conditional Autoregressive Gaussian Process for Irregularly Spaced Multivariate Data with Application to Modelling Large Sets of Binary Data

A Gaussian conditional autoregressive (CAR) formulation is presented that permits the modelling of the spatial dependence and the dependence between multivariate random variables at irregularly spaced sites so capturing some of the modelling advantages of the geostatistical approach. The model benefits not only from the explicit availability of the full conditionals but also from the computational simplicity of the precision matrix determinant calculation using a closed form expression involving the eigenvalues of a precision matrix submatrix. The introduction of covariates into the model adds little computational complexity to the analysis and thus the method can be straightforwardly extended to regression models. The model, because of its computational simplicity, is well suited to application involving the fully Bayesian analysis of large data sets involving multivariate measurements with a spatial ordering. An extension to spatio-temporal data is also considered. Here, we demonstrate use of the model in the analysis of bivariate binary data where the observed data is modelled as the sign of the hidden CAR process. A case study involving over 450 irregularly spaced sites and the presence or absence of each of two species of rain forest trees at each site is presented; Markov chain Monte Carlo (MCMC) methods are implemented to obtain posterior distributions of all unknowns. The MCMC method works well with simulated data and the tree biodiversity data set.     

Spatial hidden Markov models and species distributions

A spatial hidden Markov model (SHMM) is introduced to analyse the distribution of a species on an atlas, taking into account that false observations and false non-detections of the species can occur during the survey, blurring the true map of presence and absence of the species. The reconstruction of the true map is tackled as the restoration of a degraded pixel image, where the true map is an autologistic model, hidden behind the observed map, whose normalizing constant is efficiently computed by simulating an auxiliary map. The distribution of the species is explained under the Bayesian paradigm and Markov chain Monte Carlo (MCMC) algorithms are developed. We are interested in the spatial distribution of the bird species Greywing Francolin in the south of Africa. Many climatic and land-use explanatory variables are also available: they are included in the SHMM and a subset of them is selected by the mutation operators within the MCMC algorithm.     

FITTING SPATIAL CORRELATION MODELS: APPROXIMATING A LIKELIHOOD APPROXIMATION

The paper considers a class of spatial correlation models (stationary Gaussian processes) which includes (spatial) conditional autoregressive, simultaneous autoregressive, moving average and direct covariance models. Given observations on a finite rectangular lattice, a likelihood approximation for estimating the parameters in the spectral density of the model is discussed. The approximation consists of applying the trapezoidal rule, with a her grid of frequencies than the usual Fourier frequencies, to compute the integral in an appraximation due to Whittle (1954) and later modified by Guyon (1984). With this approximation, a Fisher scoring type algorithm has a simple form and in some casea reduces to iteratively reweighted least squares. Methods for computing the unbiased two-dimensional periodogram required by the method are presented and the accuracy of the approximation is discussed. The asymptotic distribution of the parameter estimates computed from the likelihood approximation is also given.     

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.     

Spatial effects in dynamic conditional correlations

The recent literature on time series has developed a lot of models for the analysis of the dynamic conditional correlation, involving the same variable observed in different locations; very often, in this framework, the consideration of the spatial interactions is omitted. We propose to extend a time-varying conditional correlation model (following an autoregressive moving average dynamics) to include the spatial effects, with a specification depending on the local spatial interactions. The spatial part is based on a fixed symmetric weight matrix, called Gaussian kernel matrix, but its effect will vary along the time depending on the degree of time correlation in a certain period. We show the theoretical aspects, with the support of simulation experiments, and apply this methodology to two space–time data sets, in a demographic and a financial framework, respectively.     

Lindley first-order autoregressive model with applications

ABSTRACT

A new stationary first-order autoregressive process with Lindley marginal distribution, denoted as LAR(1) is introduced. We derive the probability function for the innovation process. We consider many properties of this process, involving spectral density, some multi-step ahead conditional measures, run probabilities, stationary solution, uniqueness and ergodicity. We estimate the unknown parameters of the process using three methods of estimation and investigate properties of the estimators with some numerical results to illustrate them. Some applications of the process are discussed to two real data sets and it is shown that the LAR(1) model fits better than other known non Gaussian AR(1) models.     

Model-based segmentation of spatial cylindrical data

ABSTRACT

A new hidden Markov random field model is proposed for the analysis of cylindrical spatial series, i.e. bivariate spatial series of intensities and angles. It allows us to segment cylindrical spatial series according to a finite number of latent classes that represent the conditional distributions of the data under specific environmental conditions. The model parsimoniously accommodates circular–linear correlation, multimodality, skewness and spatial autocorrelation. A numerically tractable expectation–maximization algorithm is provided to compute parameter estimates by exploiting a mean-field approximation of the complete-data log-likelihood function. These methods are illustrated on a case study of marine currents in the Adriatic sea.     

A note on generating correlated matched-pair binary data through conditional linear family

Generating correlated binary data with specified marginal probabilities and correlation structure is often needed and useful in simulation studies to investigate the finite sample performance of statistical methods. Conditional linear family provides a powerful and flexible tool to generate correlated matched-pair binary data including the physician–patients and clustered match-pair data. To ensure the validity of the data generation process, constraints for parameters of the conditional linear family are needed. For the correlated matched-pair binary data with an exchangeable-type correlation structure, we derive the explicit expressions to check these constraints and it provides an efficient and convenient computational tool in validating the data generation process. The results are applied to check the constraints for two typical correlated matched-pair binary data.     

Max-stable processes for modeling extremes observed in space and time

Max-stable processes have proved to be useful for the statistical modeling of spatial extremes. For statistical inference it is often assumed that there is no temporal dependence; i.e., that the observations at spatial locations are independent in time. In a first approach we construct max-stable space–time processes as limits of rescaled pointwise maxima of independent Gaussian processes, where the space–time covariance functions satisfy weak regularity conditions. This leads to so-called Brown–Resnick processes. In a second approach, we extend Smith’s storm profile model to a space–time setting. We provide explicit expressions for the bivariate distribution functions, which are equal under appropriate choice of the parameters. We also show how the space–time covariance function of the underlying Gaussian process can be interpreted in terms of the tail dependence function in the limiting max-stable space–time process.     

From distance sampling to spatial capture–recapture

Distance sampling and capture–recapture are the two most widely used wildlife abundance estimation methods. capture–recapture methods have only recently incorporated models for spatial distribution and there is an increasing tendency for distance sampling methods to incorporated spatial models rather than to rely on partly design-based spatial inference. In this overview we show how spatial models are central to modern distance sampling and that spatial capture–recapture models arise as an extension of distance sampling methods. Depending on the type of data recorded, they can be viewed as particular kinds of hierarchical binary regression, Poisson regression, survival or time-to-event models, with individuals’ locations as latent variables and a spatial model as the latent variable distribution. Incorporation of spatial models in these two methods provides new opportunities for drawing explicitly spatial inferences. Areas of likely future development include more sophisticated spatial and spatio-temporal modelling of individuals’ locations and movements, new methods for integrating spatial capture–recapture and other kinds of ecological survey data, and methods for dealing with the recapture uncertainty that often arise when “capture” consists of detection by a remote device like a camera trap or microphone.     

A comparison of efficiencies between quasi-likelihood and pseudo-likelihood estimates in non-separable spatial–temporal binary data

The goal of this paper is to compare the performance of two estimation approaches, the quasi-likelihood estimating equation and the pseudo-likelihood equation, against model mis-specification for non-separable binary data. This comparison, to the authors’ knowledge, has not been done yet. In this paper, we first extend the quasi-likelihood work on spatial data to non-separable binary data. Some asymptotic properties of the quasi-likelihood estimate are also briefly discussed. We then use the techniques of a truncated Gaussian random field with a quasi-likelihood type model and a Gibbs sampler with a conditional model in the Markov random field to generate spatial–temporal binary data, respectively. For each simulated data set, both of the estimation methods are used to estimate parameters. Some discussion about the simulation results are also included.     

Predictive Inference for Big,Spatial, Non‐Gaussian Data: MODIS Cloud Data and its Change‐of‐Support

Remote sensing of the earth with satellites yields datasets that can be massive in size, nonstationary in space, and non‐Gaussian in distribution. To overcome computational challenges, we use the reduced‐rank spatial random effects (SRE) model in a statistical analysis of cloud‐mask data from NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) instrument on board NASA's Terra satellite. Parameterisations of cloud processes are the biggest source of uncertainty and sensitivity in different climate models’ future projections of Earth's climate. An accurate quantification of the spatial distribution of clouds, as well as a rigorously estimated pixel‐scale clear‐sky‐probability process, is needed to establish reliable estimates of cloud‐distributional changes and trends caused by climate change. Here we give a hierarchical spatial‐statistical modelling approach for a very large spatial dataset of 2.75 million pixels, corresponding to a granule of MODIS cloud‐mask data, and we use spatial change‐of‐Support relationships to estimate cloud fraction at coarser resolutions. Our model is non‐Gaussian; it postulates a hidden process for the clear‐sky probability that makes use of the SRE model, EM‐estimation, and optimal (empirical Bayes) spatial prediction of the clear‐sky‐probability process. Measures of prediction uncertainty are also given.     

A latent Markov model for detecting patterns of criminal activity

Summary.  The paper investigates the problem of determining patterns of criminal behaviour from official criminal histories, concentrating on the variety and type of offending convictions. The analysis is carried out on the basis of a multivariate latent Markov model which allows for discrete covariates affecting the initial and the transition probabilities of the latent process. We also show some simplifications which reduce the number of parameters substantially; we include a Rasch-like parameterization of the conditional distribution of the response variables given the latent process and a constraint of partial homogeneity of the latent Markov chain. For the maximum likelihood estimation of the model we outline an EM algorithm based on recursions known in the hidden Markov literature, which make the estimation feasible also when the number of time occasions is large. Through this model, we analyse the conviction histories of a cohort of offenders who were born in England and Wales in 1953. The final model identifies five latent classes and specifies common transition probabilities for males and females between 5-year age periods, but with different initial probabilities.     

A Bayesian prediction using the skew Gaussian distribution

A model based on the skew Gaussian distribution is presented to handle skewed spatial data. It extends the results of popular Gaussian process models. Markov chain Monte Carlo techniques are used to generate samples from the posterior distributions of the parameters. Finally, this model is applied in the spatial prediction of weekly rainfall. Cross-validation shows that the predictive performance of our model compares favorably with several kriging variants.