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Vecchia–Laplace approximations of generalized Gaussian processes for big non-Gaussian spatial data

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  • Zilber, Daniel
  • Katzfuss, Matthias

Abstract

Generalized Gaussian processes (GGPs) are highly flexible models that combine latent GPs with potentially non-Gaussian likelihoods from the exponential family. GGPs can be used in a variety of settings, including GP classification, nonparametric count regression, modeling non-Gaussian spatial data, and analyzing point patterns. However, inference for GGPs can be analytically intractable, and large datasets pose computational challenges due to the inversion of the GP covariance matrix. A Vecchia–Laplace approximation for GGPs is proposed, which combines a Laplace approximation to the non-Gaussian likelihood with a computationally efficient Vecchia approximation to the GP, resulting in simple, general, scalable, and accurate methodology. Numerical studies and comparisons on simulated and real spatial data are provided. The methods are implemented in a freely available R package.

Suggested Citation

  • Zilber, Daniel & Katzfuss, Matthias, 2021. "Vecchia–Laplace approximations of generalized Gaussian processes for big non-Gaussian spatial data," Computational Statistics & Data Analysis, Elsevier, vol. 153(C).
  • Handle: RePEc:eee:csdana:v:153:y:2021:i:c:s0167947320301729
    DOI: 10.1016/j.csda.2020.107081
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    References listed on IDEAS

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    1. Matthias Katzfuss & Joseph Guinness & Wenlong Gong & Daniel Zilber, 2020. "Vecchia Approximations of Gaussian-Process Predictions," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(3), pages 383-414, September.
    2. Abhirup Datta & Sudipto Banerjee & Andrew O. Finley & Alan E. Gelfand, 2016. "Hierarchical Nearest-Neighbor Gaussian Process Models for Large Geostatistical Datasets," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(514), pages 800-812, April.
    3. Matthew J. Heaton & Abhirup Datta & Andrew O. Finley & Reinhard Furrer & Joseph Guinness & Rajarshi Guhaniyogi & Florian Gerber & Robert B. Gramacy & Dorit Hammerling & Matthias Katzfuss & Finn Lindgr, 2019. "A Case Study Competition Among Methods for Analyzing Large Spatial Data," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 24(3), pages 398-425, September.
    4. Kaufman, Cari G. & Schervish, Mark J. & Nychka, Douglas W., 2008. "Covariance Tapering for Likelihood-Based Estimation in Large Spatial Data Sets," Journal of the American Statistical Association, American Statistical Association, vol. 103(484), pages 1545-1555.
    5. Sudipto Banerjee & Alan E. Gelfand & Andrew O. Finley & Huiyan Sang, 2008. "Gaussian predictive process models for large spatial data sets," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(4), pages 825-848, September.
    6. Wagner Hugo Bonat & Paulo Justiniano Ribeiro Jr, 2016. "Practical likelihood analysis for spatial generalized linear mixed models," Environmetrics, John Wiley & Sons, Ltd., vol. 27(2), pages 83-89, March.
    7. Håvard Rue & Sara Martino & Nicolas Chopin, 2009. "Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(2), pages 319-392, April.
    8. John Hughes & Murali Haran, 2013. "Dimension reduction and alleviation of confounding for spatial generalized linear mixed models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 75(1), pages 139-159, January.
    9. Michael L. Stein & Zhiyi Chi & Leah J. Welty, 2004. "Approximating likelihoods for large spatial data sets," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 66(2), pages 275-296, May.
    10. Finn Lindgren & Håvard Rue & Johan Lindström, 2011. "An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 73(4), pages 423-498, September.
    11. Finley, Andrew O. & Sang, Huiyan & Banerjee, Sudipto & Gelfand, Alan E., 2009. "Improving the performance of predictive process modeling for large datasets," Computational Statistics & Data Analysis, Elsevier, vol. 53(8), pages 2873-2884, June.
    12. Noel Cressie & Gardar Johannesson, 2008. "Fixed rank kriging for very large spatial data sets," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(1), pages 209-226, February.
    13. Matthias Katzfuss, 2017. "A Multi-Resolution Approximation for Massive Spatial Datasets," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 112(517), pages 201-214, January.
    14. Matthias Katzfuss & Noel Cressie, 2011. "Spatio‐temporal smoothing and EM estimation for massive remote‐sensing data sets," Journal of Time Series Analysis, Wiley Blackwell, vol. 32, pages 430-446, July.
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