IDEAS home Printed from https://ideas.repec.org/a/jss/jstsof/v063i15.html
   My bibliography  Save this article

spTimer: Spatio-Temporal Bayesian Modeling Using R

Author

Listed:
  • Bakar, Khandoker Shuvo
  • Sahu, Sujit K.

Abstract

Hierarchical Bayesian modeling of large point-referenced space-time data is increasingly becoming feasible in many environmental applications due to the recent advances in both statistical methodology and computation power. Implementation of these methods using the Markov chain Monte Carlo (MCMC) computational techniques, however, requires development of problem-specific and user-written computer code, possibly in a low-level language. This programming requirement is hindering the widespread use of the Bayesian model-based methods among practitioners and, hence there is an urgent need to develop high-level software that can analyze large data sets rich in both space and time. This paper develops the package spTimer for hierarchical Bayesian modeling of stylized environmental space-time monitoring data as a contributed software package in the R language that is fast becoming a very popular statistical computing platform. The package is able to fit, spatially and temporally predict large amounts of space-time data using three recently developed Bayesian models. The user is given control over many options regarding covariance function selection, distance calculation, prior selection and tuning of the implemented MCMC algorithms, although suitable defaults are provided. The package has many other attractive features such as on the fly transformations and an ability to spatially predict temporally aggregated summaries on the original scale, which saves the problem of storage when using MCMC methods for large datasets. A simulation example, with more than a million observations, and a real life data example are used to validate the underlying code and to illustrate the software capabilities.

Suggested Citation

  • Bakar, Khandoker Shuvo & Sahu, Sujit K., 2015. "spTimer: Spatio-Temporal Bayesian Modeling Using R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i15).
    • Handle: RePEc:jss:jstsof:v:063:i15
    DOI: http://hdl.handle.net/10.18637/jss.v063.i15
    as

    Download full text from publisher

    File URL: https://www.jstatsoft.org/index.php/jss/article/view/v063i15/v63i15.pdf
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v063i15/spTimer_2.0-0.tar.gz
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v063i15/v63i15.R
    Download Restriction: no
    File URL: https://libkey.io/http://hdl.handle.net/10.18637/jss.v063.i15?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
    ---><---

    References listed on IDEAS

    as
    1. Hadfield, Jarrod D., 2010. "MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i02).
    2. 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.
    3. Sujit K. Sahu & Alan E. Gelfand & David M. Holland, 2010. "Fusing point and areal level space–time data with application to wet deposition," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 59(1), pages 77-103, January.
    4. 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.
    5. Millo, Giovanni & Piras, Gianfranco, 2012. "splm: Spatial Panel Data Models in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 47(i01).
    6. Martin, Andrew D. & Quinn, Kevin M. & Park, Jong Hee, 2011. "MCMCpack: Markov Chain Monte Carlo in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 42(i09).
    7. Pebesma, Edzer, 2012. "spacetime: Spatio-Temporal Data in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 51(i07).
    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. Katherine A. L. Valeriano & Victor H. Lachos & Marcos O. Prates & Larissa A. Matos, 2021. "Likelihood‐based inference for spatiotemporal data with censored and missing responses," Environmetrics, John Wiley & Sons, Ltd., vol. 32(3), May.
    2. Owais Gilani & Simon Urbanek & Michael J. Kane, 2020. "Distributions of Human Exposure to Ozone During Commuting Hours in Connecticut Using the Cellular Device Network," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(1), pages 54-73, March.
    3. Yuheng Ling, 2020. "Time, space and hedonic prediction accuracy: evidence from Corsican apartment markets," The Annals of Regional Science, Springer;Western Regional Science Association, vol. 64(2), pages 367-388, April.
    4. K. Shuvo Bakar & Huidong Jin, 2018. "Spatio-temporal quantitative links between climatic extremes and population flows: a case study in the Murray-Darling Basin, Australia," Climatic Change, Springer, vol. 148(1), pages 139-153, May.
    5. K. Shuvo Bakar, 2020. "Interpolation of daily rainfall data using censored Bayesian spatially varying model," Computational Statistics, Springer, vol. 35(1), pages 135-152, March.
    6. Sabyasachi Mukhopadhyay & Joseph O. Ogutu & Gundula Bartzke & Holly T. Dublin & Hans-Peter Piepho, 2019. "Modelling Spatio-Temporal Variation in Sparse Rainfall Data Using a Hierarchical Bayesian Regression Model," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 24(2), pages 369-393, June.
    7. Pebesma, Edzer & Bivand, Roger & Ribeiro, Paulo Justiniano, 2015. "Software for Spatial Statistics," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i01).

    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. 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. Jonathan Bradley & Noel Cressie & Tao Shi, 2015. "Comparing and selecting spatial predictors using local criteria," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 24(1), pages 1-28, March.
    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. 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.
    5. Marcin Jurek & Matthias Katzfuss, 2023. "Scalable spatio‐temporal smoothing via hierarchical sparse Cholesky decomposition," Environmetrics, John Wiley & Sons, Ltd., vol. 34(1), February.
    6. Mahdi Hosseinpouri & Majid Jafari Khaledi, 2019. "An area-specific stick breaking process for spatial data," Statistical Papers, Springer, vol. 60(1), pages 199-221, February.
    7. 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.
    8. 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.
    9. 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.
    10. 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).
    11. Pebesma, Edzer & Bivand, Roger & Ribeiro, Paulo Justiniano, 2015. "Software for Spatial Statistics," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i01).
    12. 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.
    13. Qian Ren & Sudipto Banerjee, 2013. "Hierarchical Factor Models for Large Spatially Misaligned Data: A Low-Rank Predictive Process Approach," Biometrics, The International Biometric Society, vol. 69(1), pages 19-30, March.
    14. John O'Sullivan & Conor Sweeney & Andrew C. Parnell, 2020. "Bayesian spatial extreme value analysis of maximum temperatures in County Dublin, Ireland," Environmetrics, John Wiley & Sons, Ltd., vol. 31(5), August.
    15. Wagner Hugo Bonat & Bent Jørgensen, 2016. "Multivariate covariance generalized linear models," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 65(5), pages 649-675, November.
    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. Olivier Parent & Rainer Hofe, 2013. "Understanding the impact of trails on residential property values in the presence of spatial dependence," The Annals of Regional Science, Springer;Western Regional Science Association, vol. 51(2), pages 355-375, October.
    18. Sandy Burden & Noel Cressie & David G. Steel, 2015. "The SAR Model for Very Large Datasets: A Reduced Rank Approach," Econometrics, MDPI, vol. 3(2), pages 1-22, May.
    19. Wang, Craig & Furrer, Reinhard, 2021. "Combining heterogeneous spatial datasets with process-based spatial fusion models: A unifying framework," Computational Statistics & Data Analysis, Elsevier, vol. 161(C).
    20. Ryan J. Parker & Brian J. Reich & Jo Eidsvik, 2016. "A Fused Lasso Approach to Nonstationary Spatial Covariance Estimation," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 21(3), pages 569-587, September.

    More about this item

    Statistics

    Access and download statistics

    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:jss:jstsof:v:063:i15. 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: Christopher F. Baum (email available below). General contact details of provider: http://www.jstatsoft.org/ .

    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.