Spatial and spatio-temporal models with R-INLA.

During the last three decades, Bayesian methods have developed greatly in the field of epidemiology. Their main challenge focusses around computation, but the advent of Markov Chain Monte Carlo methods (MCMC) and in particular of the WinBUGS software has opened the doors of Bayesian modelling to the wide research community. However model complexity and database dimension still remain a constraint. Recently the use of Gaussian random fields has become increasingly popular in epidemiology as very often epidemiological data are characterised by a spatial and/or temporal structure which needs to be taken into account in the inferential process. The Integrated Nested Laplace Approximation (INLA) approach has been developed as a computationally efficient alternative to MCMC and the availability of an R package (R-INLA) allows researchers to easily apply this method. In this paper we review the INLA approach and present some applications on spatial and spatio-temporal data.

[1]  L. Held,et al.  Sensitivity analysis in Bayesian generalized linear mixed models for binary data , 2011 .

[2]  A. Riebler,et al.  Bayesian bivariate meta‐analysis of diagnostic test studies using integrated nested Laplace approximations , 2010, Statistics in medicine.

[3]  Håvard Rue,et al.  Implementing Approximate Bayesian Inference using Integrated Nested Laplace Approximation: a manual for the inla program , 2008 .

[4]  David Bolin,et al.  Models and Methods for Random Fields in Spatial Statistics with Computational Efficiency from Markov Properties , 2012 .

[5]  Christian P. Robert,et al.  Monte Carlo Statistical Methods , 2005, Springer Texts in Statistics.

[6]  Sander Greenland,et al.  Bayesian perspectives for epidemiological research: I. Foundations and basic methods. , 2006, International journal of epidemiology.

[7]  Gianluca Baio,et al.  Bayesian Methods in Health Economics , 2012 .

[8]  A. Gelfand,et al.  Handbook of spatial statistics , 2010 .

[9]  D B Dunson,et al.  Commentary: practical advantages of Bayesian analysis of epidemiologic data. , 2001, American journal of epidemiology.

[10]  P. Guttorp,et al.  Studies in the history of probability and statistics XLIX On the Matérn correlation family , 2006 .

[11]  Andrew Thomas,et al.  The BUGS project: Evolution, critique and future directions , 2009, Statistics in medicine.

[12]  C Pascutto,et al.  Statistical issues in the analysis of disease mapping data. , 2000, Statistics in medicine.

[14]  Håvard Rue,et al.  Direct fitting of dynamic models using integrated nested Laplace approximations - INLA , 2012, Comput. Stat. Data Anal..

[15]  James S. Clark,et al.  Why environmental scientists are becoming Bayesians , 2004 .

[16]  H. Rue,et al.  Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations , 2009 .

[17]  Haavard Rue,et al.  Think continuous: Markovian Gaussian models in spatial statistics , 2011, 1110.6796.

[18]  T. Gneiting Nonseparable, Stationary Covariance Functions for Space–Time Data , 2002 .

[19]  S. Richardson,et al.  Interpreting Posterior Relative Risk Estimates in Disease-Mapping Studies , 2004, Environmental health perspectives.

[20]  N. Cressie,et al.  Classes of nonseparable, spatio-temporal stationary covariance functions , 1999 .

[21]  Haavard Rue,et al.  Estimation and extrapolation of time trends in registry data—Borrowing strength from related populations , 2011, 1108.0606.

[22]  L. Tierney,et al.  Accurate Approximations for Posterior Moments and Marginal Densities , 1986 .

[23]  Mike Rees,et al.  5. Statistics for Spatial Data , 1993 .

[24]  Alessio Pollice,et al.  Discussing the “big n problem” , 2013, Stat. Methods Appl..

[25]  Calyampudi Radhakrishna Rao,et al.  Time series analysis : methods and applications , 2012 .

[26]  Leonhard Held,et al.  A primer on disease mapping and ecological regression using $${\texttt{INLA}}$$ , 2011, Comput. Stat..

[27]  H. Rue,et al.  In order to make spatial statistics computationally feasible, we need to forget about the covariance function , 2012 .

[28]  J. Besag,et al.  Bayesian image restoration, with two applications in spatial statistics , 1991 .

[29]  H. Rue,et al.  Approximate Bayesian inference for hierarchical Gaussian Markov random field models , 2007 .

[30]  C. Wikle Hierarchical Models in Environmental Science , 2003 .

[31]  Sw. Banerjee,et al.  Hierarchical Modeling and Analysis for Spatial Data , 2003 .

[32]  D. Cocchi,et al.  Hierarchical space-time modelling of PM10 pollution , 2007 .

[33]  Finn Lindgren,et al.  Bayesian computing with INLA: New features , 2012, Comput. Stat. Data Anal..

[34]  Andrew Gelman,et al.  The No-U-turn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo , 2011, J. Mach. Learn. Res..

[35]  M. Dolores Ugarte,et al.  Statistical Methods for Spatio-temporal Systems , 2006 .

[36]  S. Finardi,et al.  A deterministic air quality forecasting system for Torino urban area, Italy , 2008, Environ. Model. Softw..

[37]  L Knorr-Held,et al.  Bayesian modelling of inseparable space-time variation in disease risk. , 2000, Statistics in medicine.

[38]  Peter Congdon Bayesian statistical modelling , 2002 .

[39]  Michela Cameletti,et al.  Comparing spatio‐temporal models for particulate matter in Piemonte , 2011 .

[40]  Patrick Brown,et al.  Spatial modelling of lupus incidence over 40 years with changes in census areas , 2012 .

[41]  Sujit K. Sahu,et al.  Hierarchical Bayesian models for space-time air pollution data , 2012 .

[42]  Bradley P. Carlin,et al.  Bayesian measures of model complexity and fit , 2002 .

[43]  Alessandro Fasso,et al.  Maximum likelihood estimation of the dynamic coregionalization model with heterotopic data , 2011 .

[44]  M. Girolami,et al.  Riemann manifold Langevin and Hamiltonian Monte Carlo methods , 2011, Journal of the Royal Statistical Society: Series B (Statistical Methodology).

[45]  Leonhard Held,et al.  Spatio‐temporal disease mapping using INLA , 2011 .

[46]  Neal Alexander,et al.  Bayesian Disease Mapping: Hierarchical Modeling in Spatial Epidemiology , 2011 .

[47]  Leonhard Held,et al.  Gaussian Markov Random Fields: Theory and Applications , 2005 .

[48]  Edzer J. Pebesma,et al.  Multivariable geostatistics in S: the gstat package , 2004, Comput. Geosci..

[49]  Han Lin Shang,et al.  The BUGS book: a practical introduction to Bayesian analysis , 2013 .

[50]  Bradley P. Carlin,et al.  Bayesian Adaptive Methods for Clinical Trials , 2010 .

[51]  H. Rue,et al.  Spatio-temporal modeling of particulate matter concentration through the SPDE approach , 2012, AStA Advances in Statistical Analysis.

[52]  S D.,et al.  Going off grid: Computationally efficient inference for log-Gaussian Cox processes , 2015 .

[53]  Haavard Rue,et al.  Going off grid: computationally efficient inference for log-Gaussian Cox processes , 2016 .

[54]  D. Clayton,et al.  Bayesian analysis of space-time variation in disease risk. , 1995, Statistics in medicine.

[55]  Leonhard Held,et al.  Using integrated nested Laplace approximations for the evaluation of veterinary surveillance data from Switzerland: a case‐study , 2011 .

[56]  G. Roberts,et al.  Bayesian analysis for emerging infectious diseases , 2009 .

[57]  P. Diggle,et al.  Model‐based geostatistics , 2007 .

[58]  Andrew Gelman,et al.  Handbook of Markov Chain Monte Carlo , 2011 .

[59]  Simon Jackman,et al.  Bayesian Analysis for the Social Sciences , 2009 .

[60]  Jane L. Harvill Spatio‐temporal processes , 2010 .

[61]  H. Rue,et al.  An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach , 2011 .

[62]  Noel A Cressie,et al.  Statistics for Spatial Data. , 1992 .

[63]  James S. Clark,et al.  Hierarchical Modelling for the Environmental Sciences: Statistical Methods and Applications , 2006 .

[64]  Kjersti Aas,et al.  Norges Teknisk-naturvitenskapelige Universitet Estimating Stochastic Volatility Models Using Integrated Nested Laplace Approximations Estimating Stochastic Volatility Models Using Integrated Nested Laplace Approximations , 2022 .