IDEAS home Printed from https://ideas.repec.org/a/spr/jagbes/v24y2019i3d10.1007_s13253-018-00348-w.html
   My bibliography  Save this article

A Case Study Competition Among Methods for Analyzing Large Spatial Data

Author

Listed:
  • Matthew J. Heaton

    (Brigham Young University)

  • Abhirup Datta

    (Brigham Young University)

  • Andrew O. Finley

    (Brigham Young University)

  • Reinhard Furrer

    (Brigham Young University)

  • Joseph Guinness

    (Brigham Young University)

  • Rajarshi Guhaniyogi

    (Brigham Young University)

  • Florian Gerber

    (Brigham Young University)

  • Robert B. Gramacy

    (Brigham Young University)

  • Dorit Hammerling

    (Brigham Young University)

  • Matthias Katzfuss

    (Brigham Young University)

  • Finn Lindgren

    (Brigham Young University)

  • Douglas W. Nychka

    (Brigham Young University)

  • Furong Sun

    (Brigham Young University)

  • Andrew Zammit-Mangion

    (Brigham Young University)

Abstract

The Gaussian process is an indispensable tool for spatial data analysts. The onset of the “big data” era, however, has lead to the traditional Gaussian process being computationally infeasible for modern spatial data. As such, various alternatives to the full Gaussian process that are more amenable to handling big spatial data have been proposed. These modern methods often exploit low-rank structures and/or multi-core and multi-threaded computing environments to facilitate computation. This study provides, first, an introductory overview of several methods for analyzing large spatial data. Second, this study describes the results of a predictive competition among the described methods as implemented by different groups with strong expertise in the methodology. Specifically, each research group was provided with two training datasets (one simulated and one observed) along with a set of prediction locations. Each group then wrote their own implementation of their method to produce predictions at the given location and each was subsequently run on a common computing environment. The methods were then compared in terms of various predictive diagnostics. Supplementary materials regarding implementation details of the methods and code are available for this article online.

Suggested Citation

  • 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.
  • Handle: RePEc:spr:jagbes:v:24:y:2019:i:3:d:10.1007_s13253-018-00348-w
    DOI: 10.1007/s13253-018-00348-w
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s13253-018-00348-w
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1007/s13253-018-00348-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Brian Neelon & Alan E. Gelfand & Marie Lynn Miranda, 2014. "A multivariate spatial mixture model for areal data: examining regional differences in standardized test scores," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 63(5), pages 737-761, November.
    2. Kang, Emily L. & Cressie, Noel, 2011. "Bayesian Inference for the Spatial Random Effects Model," Journal of the American Statistical Association, American Statistical Association, vol. 106(495), pages 972-983.
    3. 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.
    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. Kang, Emily L. & Liu, Desheng & Cressie, Noel, 2009. "Statistical analysis of small-area data based on independence, spatial, non-hierarchical, and hierarchical models," Computational Statistics & Data Analysis, Elsevier, vol. 53(8), pages 3016-3032, June.
    7. Faming Liang & Yichen Cheng & Qifan Song & Jincheol Park & Ping Yang, 2013. "A Resampling-Based Stochastic Approximation Method for Analysis of Large Geostatistical Data," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 108(501), pages 325-339, March.
    8. Fuentes, Montserrat, 2007. "Approximate Likelihood for Large Irregularly Spaced Spatial Data," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 321-331, March.
    9. Toshihiro Hirano & Yoshihiro Yajima, 2013. "Covariance tapering for prediction of large spatial data sets in transformed random fields," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 65(5), pages 913-939, October.
    10. 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.
    11. Leonhard Knorr-Held & Günter Raßer, 2000. "Bayesian Detection of Clusters and Discontinuities in Disease Maps," Biometrics, The International Biometric Society, vol. 56(1), pages 13-21, March.
    12. 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.
    13. 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.
    14. 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.
    15. Kim, Hyoung-Moon & Mallick, Bani K. & Holmes, C.C., 2005. "Analyzing Nonstationary Spatial Data Using Piecewise Gaussian Processes," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 653-668, June.
    16. Wenceslao González‐Manteiga & Rosa M. Crujeiras & Daniel Simpson & Finn Lindgren & Håvard Rue, 2012. "In order to make spatial statistics computationally feasible, we need to forget about the covariance function," Environmetrics, John Wiley & Sons, Ltd., vol. 23(1), pages 65-74, February.
    17. Gramacy, Robert B., 2016. "laGP: Large-Scale Spatial Modeling via Local Approximate Gaussian Processes in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 72(i01).
    18. Furrer, Reinhard & Sain, Stephan R., 2010. "spam: A Sparse Matrix R Package with Emphasis on MCMC Methods for Gaussian Markov Random Fields," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 36(i10).
    19. Gneiting, Tilmann & Raftery, Adrian E., 2007. "Strictly Proper Scoring Rules, Prediction, and Estimation," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 359-378, March.
    20. Huiyan Sang & Jianhua Z. Huang, 2012. "A full scale approximation of covariance functions for large spatial data sets," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 74(1), pages 111-132, January.
    21. 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.
    22. Paciorek, Christopher J. & Lipshitz, Benjamin & Zhuo, Wei & Prabhat, . & Kaufman, Cari G. G. & Thomas, Rollin C., 2015. "Parallelizing Gaussian Process Calculations in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i10).
    23. 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.
    24. Furrer, Reinhard & Bachoc, François & Du, Juan, 2016. "Asymptotic properties of multivariate tapering for estimation and prediction," Journal of Multivariate Analysis, Elsevier, vol. 149(C), pages 177-191.
    25. Lemos, Ricardo T. & Sansó, Bruno, 2009. "A Spatio-Temporal Model for Mean, Anomaly, and Trend Fields of North Atlantic Sea Surface Temperature," Journal of the American Statistical Association, American Statistical Association, vol. 104(485), pages 5-18.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. May, Paul & Biesecker, Matthew & Rekabdarkolaee, Hossein Moradi, 2022. "Response envelopes for linear coregionalization models," Journal of Multivariate Analysis, Elsevier, vol. 192(C).
    2. Huang, Whitney K. & Chung, Yu-Min & Wang, Yu-Bo & Mandel, Jeff E. & Wu, Hau-Tieng, 2022. "Airflow recovery from thoracic and abdominal movements using synchrosqueezing transform and locally stationary Gaussian process regression," Computational Statistics & Data Analysis, Elsevier, vol. 174(C).
    3. Paige, John & Fuglstad, Geir-Arne & Riebler, Andrea & Wakefield, Jon, 2022. "Bayesian multiresolution modeling of georeferenced data: An extension of ‘LatticeKrig’," Computational Statistics & Data Analysis, Elsevier, vol. 173(C).
    4. 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.
    5. 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).
    6. Margaret C Johnson & Brian J Reich & Josh M Gray, 2021. "Multisensor fusion of remotely sensed vegetation indices using space‐time dynamic linear models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(3), pages 793-812, June.
    7. Quan Vu & Yi Cao & Josh Jacobson & Alan R. Pearse & Andrew Zammit-Mangion, 2021. "Discussion on “Competition on Spatial Statistics for Large Datasets”," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(4), pages 614-618, December.
    8. Morales-Oñate, Víctor & Crudu, Federico & Bevilacqua, Moreno, 2021. "Blockwise Euclidean likelihood for spatio-temporal covariance models," Econometrics and Statistics, Elsevier, vol. 20(C), pages 176-201.
    9. Jialuo Liu & Tingjin Chu & Jun Zhu & Haonan Wang, 2022. "Large spatial data modeling and analysis: A Krylov subspace approach," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 49(3), pages 1115-1143, September.
    10. Moreno Bevilacqua & Christian Caamaño‐Carrillo & Carlo Gaetan, 2020. "On modeling positive continuous data with spatiotemporal dependence," Environmetrics, John Wiley & Sons, Ltd., vol. 31(7), November.
    11. Jennifer F. Bobb & Maricela F. Cruz & Stephen J. Mooney & Adam Drewnowski & David Arterburn & Andrea J. Cook, 2022. "Accounting for spatial confounding in epidemiological studies with individual‐level exposures: An exposure‐penalized spline approach," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 185(3), pages 1271-1293, July.
    12. Huang Huang & Sameh Abdulah & Ying Sun & Hatem Ltaief & David E. Keyes & Marc G. Genton, 2021. "Competition on Spatial Statistics for Large Datasets," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(4), pages 580-595, December.
    13. Acosta, Jonathan & Alegría, Alfredo & Osorio, Felipe & Vallejos, Ronny, 2021. "Assessing the effective sample size for large spatial datasets: A block likelihood approach," Computational Statistics & Data Analysis, Elsevier, vol. 162(C).
    14. Dorit Hammerling & Brian J. Reich, 2019. "Guest Editors’ Introduction to the Special Issue on “Climate and the Earth System”," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 24(3), pages 395-397, September.
    15. Eric W Fox & Jay M Ver Hoef & Anthony R Olsen, 2020. "Comparing spatial regression to random forests for large environmental data sets," PLOS ONE, Public Library of Science, vol. 15(3), pages 1-22, March.
    16. Lu Zhang & Sudipto Banerjee & Andrew O. Finley, 2021. "High‐dimensional multivariate geostatistics: A Bayesian matrix‐normal approach," Environmetrics, John Wiley & Sons, Ltd., vol. 32(4), June.
    17. Felipe Tagle & Marc G. Genton & Andrew Yip & Suleiman Mostamandi & Georgiy Stenchikov & Stefano Castruccio, 2020. "A high‐resolution bilevel skew‐t stochastic generator for assessing Saudi Arabia's wind energy resources," Environmetrics, John Wiley & Sons, Ltd., vol. 31(7), November.
    18. Bevilacqua, Moreno & Caamaño-Carrillo, Christian & Porcu, Emilio, 2022. "Unifying compactly supported and Matérn covariance functions in spatial statistics," Journal of Multivariate Analysis, Elsevier, vol. 189(C).
    19. Zhou Lan & Brian J. Reich & Joseph Guinness & Dipankar Bandyopadhyay & Liangsuo Ma & F. Gerard Moeller, 2022. "Geostatistical modeling of positive‐definite matrices: An application to diffusion tensor imaging," Biometrics, The International Biometric Society, vol. 78(2), pages 548-559, June.
    20. Jakob A. Dambon & Stefan S. Fahrländer & Saira Karlen & Manuel Lehner & Jaron Schlesinger & Fabio Sigrist & Anna Zimmermann, 2022. "Examining the vintage effect in hedonic pricing using spatially varying coefficients models: a case study of single-family houses in the Canton of Zurich," Swiss Journal of Economics and Statistics, Springer;Swiss Society of Economics and Statistics, vol. 158(1), pages 1-14, December.
    21. Lu Zhang & Sudipto Banerjee, 2022. "Spatial factor modeling: A Bayesian matrix‐normal approach for misaligned data," Biometrics, The International Biometric Society, vol. 78(2), pages 560-573, June.
    22. Arthur P. Guillaumin & Adam M. Sykulski & Sofia C. Olhede & Frederik J. Simons, 2022. "The Debiased Spatial Whittle likelihood," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 84(4), pages 1526-1557, September.
    23. Ashton Wiens & Douglas Nychka & William Kleiber, 2020. "Modeling spatial data using local likelihood estimation and a Matérn to spatial autoregressive translation," Environmetrics, John Wiley & Sons, Ltd., vol. 31(6), September.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sameh Abdulah & Yuxiao Li & Jian Cao & Hatem Ltaief & David E. Keyes & Marc G. Genton & Ying Sun, 2023. "Large‐scale environmental data science with ExaGeoStatR," Environmetrics, John Wiley & Sons, Ltd., vol. 34(1), February.
    2. 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).
    3. 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.
    4. Eidsvik, Jo & Finley, Andrew O. & Banerjee, Sudipto & Rue, Håvard, 2012. "Approximate Bayesian inference for large spatial datasets using predictive process models," Computational Statistics & Data Analysis, Elsevier, vol. 56(6), pages 1362-1380.
    5. Jialuo Liu & Tingjin Chu & Jun Zhu & Haonan Wang, 2022. "Large spatial data modeling and analysis: A Krylov subspace approach," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 49(3), pages 1115-1143, September.
    6. Giovanna Jona Lasinio & Gianluca Mastrantonio & Alessio Pollice, 2013. "Discussing the “big n problem”," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 22(1), pages 97-112, March.
    7. Chen, Yewen & Chang, Xiaohui & Luo, Fangzhi & Huang, Hui, 2023. "Additive dynamic models for correcting numerical model outputs," Computational Statistics & Data Analysis, Elsevier, vol. 187(C).
    8. Bledar A. Konomi & Emily L. Kang & Ayat Almomani & Jonathan Hobbs, 2023. "Bayesian Latent Variable Co-kriging Model in Remote Sensing for Quality Flagged Observations," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 28(3), pages 423-441, September.
    9. 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.
    10. Huang Huang & Sameh Abdulah & Ying Sun & Hatem Ltaief & David E. Keyes & Marc G. Genton, 2021. "Competition on Spatial Statistics for Large Datasets," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 26(4), pages 580-595, December.
    11. Jingjie Zhang & Matthias Katzfuss, 2022. "Multi-Scale Vecchia Approximations of Gaussian Processes," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 27(3), pages 440-460, September.
    12. Guhaniyogi, Rajarshi & Banerjee, Sudipto, 2019. "Multivariate spatial meta kriging," Statistics & Probability Letters, Elsevier, vol. 144(C), pages 3-8.
    13. Litvinenko, Alexander & Sun, Ying & Genton, Marc G. & Keyes, David E., 2019. "Likelihood approximation with hierarchical matrices for large spatial datasets," Computational Statistics & Data Analysis, Elsevier, vol. 137(C), pages 115-132.
    14. Shinichiro Shirota & Andrew O. Finley & Bruce D. Cook & Sudipto Banerjee, 2023. "Conjugate sparse plus low rank models for efficient Bayesian interpolation of large spatial data," Environmetrics, John Wiley & Sons, Ltd., vol. 34(1), February.
    15. Peter A. Gao & Hannah M. Director & Cecilia M. Bitz & Adrian E. Raftery, 2022. "Probabilistic Forecasts of Arctic Sea Ice Thickness," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 27(2), pages 280-302, June.
    16. Waley W. J. Liang & Herbert K. H. Lee, 2019. "Bayesian nonstationary Gaussian process models via treed process convolutions," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 13(3), pages 797-818, September.
    17. Marchetti, Yuliya & Nguyen, Hai & Braverman, Amy & Cressie, Noel, 2018. "Spatial data compression via adaptive dispersion clustering," Computational Statistics & Data Analysis, Elsevier, vol. 117(C), pages 138-153.
    18. Furrer, Reinhard & Bachoc, François & Du, Juan, 2016. "Asymptotic properties of multivariate tapering for estimation and prediction," Journal of Multivariate Analysis, Elsevier, vol. 149(C), pages 177-191.
    19. Bevilacqua, Moreno & Caamaño-Carrillo, Christian & Porcu, Emilio, 2022. "Unifying compactly supported and Matérn covariance functions in spatial statistics," Journal of Multivariate Analysis, Elsevier, vol. 189(C).
    20. Arthur P. Guillaumin & Adam M. Sykulski & Sofia C. Olhede & Frederik J. Simons, 2022. "The Debiased Spatial Whittle likelihood," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 84(4), pages 1526-1557, September.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:jagbes:v:24:y:2019:i:3:d:10.1007_s13253-018-00348-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.