Statistics for Spatial Data.

Bayesian methods have garnered huge interest in cognitive science as an approach to models of cognition and perception. On the other hand, Bayesian methods for data analysis have not yet made much headway in cognitive science against the institutionalized inertia of 20th century null hypothesis significance testing (NHST). Ironically, specific Bayesian models of cognition and perception may not long endure the ravages of empirical verification, but generic Bayesian methods for data analysis will eventually dominate. It is time that Bayesian data analysis became the norm for empirical methods in cognitive science. This article reviews a fatal flaw of NHST and introduces the reader to some benefits of Bayesian data analysis. The article presents illustrative examples of multiple comparisons in Bayesian analysis of variance and Bayesian approaches to statistical power. Copyright © 2010 John Wiley & Sons, Ltd. For further resources related to this article, please visit the WIREs website.

Bayesian data analysis.

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

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Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

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

Abstract A two-dimensional version of the Pennsylvania State University mesoscale model has been applied to Winter Monsoon Experiment data in order to simulate the diurnally occurring convection observed over the South China Sea. The domain includes a representation of part of Borneo as well as the sea so that the model can simulate the initiation of convection. Also included in the model are parameterizations of mesoscale ice phase and moisture processes and longwave and shortwave radiation with a diurnal cycle. This allows use of the model to test the relative importance of various heating mechanisms to the stratiform cloud deck, which typically occupies several hundred kilometers of the domain. Frank and Cohen's cumulus parameterization scheme is employed to represent vital unresolved vertical transports in the convective area. The major conclusions are: Ice phase processes are important in determining the level of maximum large-scale heating and vertical motion because there is a strong anvil componen...

Numerical study of convection observed during the Winter Monsoon Experiment using a mesoscale two-dimensional model [presentation]

(2005). Atmospheric Modeling, Data Assimilation, and Predictability. Technometrics: Vol. 47, No. 4, pp. 521-521.

Atmospheric Modeling, Data Assimilation, and Predictability

Statistics for Spatio-Temporal Data

Analyses of ecological data should account for the uncertainty in the process(es) that generated the data. However, accounting for these uncertainties is a difficult task, since ecology is known for its complexity. Measurement and/or process errors are often the only sources of uncertainty modeled when addressing complex ecological problems, yet analyses should also account for uncertainty in sampling design, in model specification, in parameters governing the specified model, and in initial and boundary conditions. Only then can we be confident in the scientific inferences and forecasts made from an analysis. Probability and statistics provide a framework that accounts for multiple sources of uncertainty. Given the complexities of ecological studies, the hierarchical statistical model is an invaluable tool. This approach is not new in ecology, and there are many examples (both Bayesian and non-Bayesian) in the literature illustrating the benefits of this approach. In this article, we provide a baseline for concepts, notation, and methods, from which discussion on hierarchical statistical modeling in ecology can proceed. We have also planted some seeds for discussion and tried to show where the practical difficulties lie. Our thesis is that hierarchical statistical modeling is a powerful way of approaching ecological analysis in the presence of inevitable but quantifiable uncertainties, even if practical issues sometimes require pragmatic compromises.

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Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling

SUMMARY Many physical/biological processes involve variability over both space and time. As a result of difficulties caused by large datasets and the modelling of space, time and spatiotemporal interactions, traditional space-time methods are limited. In this paper, we present an approach to space-time prediction that achieves dimension reduction and uses a statistical model that is temporally dynamic and spatially descriptive. That is, it exploits the unidirectional flow of time, in an autoregressive framework, and is spatially 'descriptive' in that the autoregressive process is spatially coloured. With the inclusion of a measurement equation, this formulation naturally leads to the development of a spatio-temporal Kalman filter that achieves dimension reduction in the analysis of large spatio-temporal datasets. Unlike other recent space-time Kalman filters, our model also allows a nondynamic spatial component. The method is applied to a dataset of near-surface winds over the topical Pacific ocean. Spatial predictions with this dataset are improved by considering the additional non-dynamic spatial process. The improvement becomes more pronounced as the signal-to-noise ratio decreases.

A dimension-reduced approach to space-time Kalman filtering

Space-time data are ubiquitous in the environmental sciences. Often, as is the case with atmo- spheric and oceanographic processes, these data contain many different scales of spatial and temporal variability. Such data are often non-stationary in space and time and may involve many observation/prediction locations. These factors can limit the effectiveness of traditional space- time statistical models and methods. In this article, we propose the use of hierarchical space-time models to achieve more flexible models and methods for the analysis of environmental data distributed in space and time. The first stage of the hierarchical model specifies a measurement- error process for the observational data in terms of some 'state' process. The second stage allows for site-specific time series models for this state variable. This stage includes large-scale (e.g. seasonal) variability plus a space-time dynamic process for the ’anomalies'. Much of our interest is with this anomaly proc ess. In the third stage, the parameters of these time series models, which are distributed in space, are themselves given a joint distribution with spatial dependence (Markov random fields). The Bayesian formulation is completed in the last two stages by speci- fying priors on parameters. We implement the model in a Markov chain Monte Carlo framework and apply it to an atmospheric data set of monthly maximum temperature.

Christopher K. Wikle

Papers

Atmospheric Modeling, Data Assimilation, and Predictability

Statistics for Spatio-Temporal Data

Accounting for uncertainty in ecological analysis: the strengths and limitations of hierarchical statistical modeling

A dimension-reduced approach to space-time Kalman filtering

Hierarchical Bayesian space-time models