Statistical approaches to overdispersion, correlated errors, shrinkage estimation, and smoothing of regression relationships may be encompassed within the framework of the generalized linear mixed model (GLMM). Given an unobserved vector of random effects, observations are assumed to be conditionally independent with means that depend on the linear predictor through a specified link function and conditional variances that are specified by a variance function, known prior weights and a scale factor. The random effects are assumed to be normally distributed with mean zero and dispersion matrix depending on unknown variance components. For problems involving time series, spatial aggregation and smoothing, the dispersion may be specified in terms of a rank deficient inverse covariance matrix. Approximation of the marginal quasi-likelihood using Laplace's method leads eventually to estimating equations based on penalized quasilikelihood or PQL for the mean parameters and pseudo-likelihood for the variances. Im...

https://www.jstor.org/stable/pdfplus/2290687.pdf

Approximate inference in generalized linear mixed models

Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.

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Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations

Species distributional or trait data based on range map (extent-of-occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method’s implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing

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Methods to account for spatial autocorrelation in the analysis of species distributional data : a review

An overview of model-based geostatistics.- Gaussian models for geostatistical data.- Generalized linear models for geostatistical data.- Classical parameter estimation.- Spatial prediction.- Bayesian inference.- Geostatistical design.

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Model-based Geostatistics

Summary. A general class of statistical models for a univariate response variable is presented which we call the generalized additive model for location, scale and shape (GAMLSS). The model assumes independent observations of the response variable y given the parameters, the explanatory variables and the values of the random effects. The distribution for the response variable in the GAMLSS can be selected from a very general family of distributions including highly skew or kurtotic continuous and discrete distributions. The systematic part of the model is expanded to allow modelling not only of the mean (or location) but also of the other parameters of the distribution of y, as parametric and/or additive nonparametric (smooth) functions of explanatory variables and/or random-effects terms. Maximum (penalized) likelihood estimation is used to fit the (non)parametric models. A Newton–Raphson or Fisher scoring algorithm is used to maximize the (penalized) likelihood. The additive terms in the model are fitted by using a backfitting algorithm. Censored data are easily incorporated into the framework. Five data sets from different fields of application are analysed to emphasize the generality of the GAMLSS class of models.

https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1467-9876.2005.00510.x

Generalized additive models for location, scale and shape

There has been much recent interest in Bayesian image analysis, including such topics as removal of blur and noise, detection of object boundaries, classification of textures, and reconstruction of two- or three-dimensional scenes from noisy lower-dimensional views. Perhaps the most straightforward task is that of image restoration, though it is often suggested that this is an area of relatively minor practical importance. The present paper argues the contrary, since many problems in the analysis of spatial data can be interpreted as problems of image restoration. Furthermore, the amounts of data involved allow routine use of computer intensive methods, such as the Gibbs sampler, that are not yet practicable for conventional images. Two examples are given, one in archeology, the other in epidemiology. These are preceded by a partial review of pixel-based Bayesian image analysis.

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Bayesian image restoration, with two applications in spatial statistics

Radioactive thorium wastes were found in April 1997 at the former industrial site of 'Orflam-Plast' in the commune of Pargny sur Saulx in the Northeast of France, where industrial activity began in 1934. On this site, between 1934 and 1970, cerium for lighter stones and thorium nitrate were extracted from imported monazite sand, a mineral containing elevated levels of natural radioactivity. We decided to study cancer mortality in the surrounding population. We found an excess of mortality due to lung and bladder cancer in the commune of Pargny sur Saulx and its neighbours, between 1968 and 1994. This excess did not seem to be linked to the river of Saulx which was a possible source of contamination. We conclude that a cancer incidence study of the former workers of this industrial site is necessary in order to investigate the role of natural radioactivity from monazite processing in the risk of cancer mortality among this workforce.

Annie Mollié

Papers

Bayesian image restoration, with two applications in spatial statistics

Cancer mortality in the commune of Pargny sur Saulx in France