IDEAS home Printed from https://ideas.repec.org/a/spr/compst/v33y2018i4d10.1007_s00180-018-0805-z.html
   My bibliography  Save this article

sppmix: Poisson point process modeling using normal mixture models

Author

Listed:
  • Athanasios C. Micheas

    (University of Missouri-Columbia)

  • Jiaxun Chen

    (University of Missouri-Columbia)

Abstract

This paper describes the package sppmix for the statistical environment R. The sppmix package implements classes and methods for modeling spatial point patterns using inhomogeneous Poisson point processes, where the intensity surface is assumed to be a multiple of a finite additive mixture of normal components and the number of components is a finite, fixed or random integer. Extensions to the marked inhomogeneous Poisson point processes case are also presented. We provide an extensive suite of R functions that can be used to simulate, visualize and model point patterns, estimate the parameters of the models, assess convergence of the algorithms and perform model selection and checking in the proposed modeling context. In addition, several approaches have been implemented in order to handle the standard label switching issue which arises in any modeling approach involving mixture models. We adapt a hierarchical Bayesian framework in order to model the intensity surfaces and have implemented two major algorithms in order to estimate the parameters of the mixture models involved: the data augmentation and the birth–death Markov chain Monte Carlo (DAMCMC and BDMCMC). We used C++ (via the Rcpp package) in order to implement the most computationally intensive algorithms.

Suggested Citation

  • Athanasios C. Micheas & Jiaxun Chen, 2018. "sppmix: Poisson point process modeling using normal mixture models," Computational Statistics, Springer, vol. 33(4), pages 1767-1798, December.
  • Handle: RePEc:spr:compst:v:33:y:2018:i:4:d:10.1007_s00180-018-0805-z
    DOI: 10.1007/s00180-018-0805-z
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s00180-018-0805-z
    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/s00180-018-0805-z?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. Athanasios Christou Micheas, 2014. "Hierarchical Bayesian modeling of marked non-homogeneous Poisson processes with finite mixtures and inclusion of covariate information," Journal of Applied Statistics, Taylor & Francis Journals, vol. 41(12), pages 2596-2615, December.
    2. Stephen L. Rathbun & Saul Shiffman & Chad J. Gwaltney, 2007. "Modelling the effects of partially observed covariates on Poisson process intensity," Biometrika, Biometrika Trust, vol. 94(1), pages 153-165.
    3. repec:dau:papers:123456789/6069 is not listed on IDEAS
    4. Eddelbuettel, Dirk & Francois, Romain, 2011. "Rcpp: Seamless R and C++ Integration," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 40(i08).
    5. Olivier Cappé & Christian P. Robert & Tobias Rydén, 2003. "Reversible jump, birth‐and‐death and more general continuous time Markov chain Monte Carlo samplers," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 65(3), pages 679-700, August.
    6. Eddelbuettel, Dirk & Sanderson, Conrad, 2014. "RcppArmadillo: Accelerating R with high-performance C++ linear algebra," Computational Statistics & Data Analysis, Elsevier, vol. 71(C), pages 1054-1063.
    7. Taylor, Benjamin M. & Davies, Tilman M. & Rowlingson, Barry S. & Diggle, Peter J., 2015. "Bayesian Inference and Data Augmentation Schemes for Spatial, Spatiotemporal and Multivariate Log-Gaussian Cox Processes in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i07).
    8. Sylvia. Richardson & Peter J. Green, 1997. "On Bayesian Analysis of Mixtures with an Unknown Number of Components (with discussion)," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 59(4), pages 731-792.
    9. 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.
    10. repec:dau:papers:123456789/6040 is not listed on IDEAS
    11. 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.
    12. Jesper Møller & Kateřina Helisová, 2010. "Likelihood Inference for Unions of Interacting Discs," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 37(3), pages 365-381, September.
    13. Taylor, Benjamin M. & Davies, Tilman M. & Rowlingson, Barry S. & Diggle, Peter J., 2013. "lgcp: An R Package for Inference with Spatial and Spatio-Temporal Log-Gaussian Cox Processes," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 52(i04).
    14. Zhengyi Zhou & David S. Matteson & Dawn B. Woodard & Shane G. Henderson & Athanasios C. Micheas, 2015. "A Spatio-Temporal Point Process Model for Ambulance Demand," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(509), pages 6-15, March.
    15. Jesper Møller & Rasmus P. Waagepetersen, 2007. "Modern Statistics for Spatial Point Processes," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 34(4), pages 643-684, December.
    16. Hossain, Md. Monir & Lawson, Andrew B., 2009. "Approximate methods in Bayesian point process spatial models," Computational Statistics & Data Analysis, Elsevier, vol. 53(8), pages 2831-2842, June.
    17. Baddeley, Adrian & Turner, Rolf, 2005. "spatstat: An R Package for Analyzing Spatial Point Patterns," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 12(i06).
    Full references (including those not matched with items on IDEAS)

    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. Athanasios Christou Micheas, 2014. "Hierarchical Bayesian modeling of marked non-homogeneous Poisson processes with finite mixtures and inclusion of covariate information," Journal of Applied Statistics, Taylor & Francis Journals, vol. 41(12), pages 2596-2615, December.
    2. Janine B. Illian & David F. R. P. Burslem, 2017. "Improving the usability of spatial point process methodology: an interdisciplinary dialogue between statistics and ecology," AStA Advances in Statistical Analysis, Springer;German Statistical Society, vol. 101(4), pages 495-520, October.
    3. Brown, Patrick E., 2015. "Model-Based Geostatistics the Easy Way," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i12).
    4. Kenneth A. Flagg & Andrew Hoegh & John J. Borkowski, 2020. "Modeling Partially Surveyed Point Process Data: Inferring Spatial Point Intensity of Geomagnetic Anomalies," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 25(2), pages 186-205, June.
    5. Williamson, Laura D. & Scott, Beth E. & Laxton, Megan & Illian, Janine B. & Todd, Victoria L.G. & Miller, Peter I. & Brookes, Kate L., 2022. "Comparing distribution of harbour porpoise using generalized additive models and hierarchical Bayesian models with integrated nested laplace approximation," Ecological Modelling, Elsevier, vol. 470(C).
    6. Taylor, Benjamin M. & Rowlingson, Barry S., 2017. "spatsurv: An R Package for Bayesian Inference with Spatial Survival Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 77(i04).
    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).
    8. Taylor, Benjamin M. & Davies, Tilman M. & Rowlingson, Barry S. & Diggle, Peter J., 2015. "Bayesian Inference and Data Augmentation Schemes for Spatial, Spatiotemporal and Multivariate Log-Gaussian Cox Processes in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i07).
    9. Humphreys, John M. & Elsner, James B. & Jagger, Thomas H. & Pau, Stephanie, 2017. "A Bayesian geostatistical approach to modeling global distributions of Lygodium microphyllum under projected climate warming," Ecological Modelling, Elsevier, vol. 363(C), pages 192-206.
    10. 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.
    11. Jing, Liang & De Oliveira, Victor, 2015. "geoCount: An R Package for the Analysis of Geostatistical Count Data," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 63(i11).
    12. Wilson J. Wright & Peter N. Neitlich & Alyssa E. Shiel & Mevin B. Hooten, 2022. "Mechanistic spatial models for heavy metal pollution," Environmetrics, John Wiley & Sons, Ltd., vol. 33(8), December.
    13. Andre Python & Andreas Bender & Marta Blangiardo & Janine B. Illian & Ying Lin & Baoli Liu & Tim C.D. Lucas & Siwei Tan & Yingying Wen & Davit Svanidze & Jianwei Yin, 2022. "A downscaling approach to compare COVID‐19 count data from databases aggregated at different spatial scales," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 185(1), pages 202-218, January.
    14. Michaela Prokešová & Eva Jensen, 2013. "Asymptotic Palm likelihood theory for stationary point processes," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 65(2), pages 387-412, April.
    15. Daniela Silva & Raquel Menezes & Ana Moreno & Ana Teles-Machado & Susana Garrido, 2024. "Environmental Effects on the Spatiotemporal Variability of Sardine Distribution Along the Portuguese Continental Coast," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 29(3), pages 553-575, September.
    16. Yuan Yan & Eva Cantoni & Chris Field & Margaret Treble & Joanna Mills Flemming, 2023. "Spatiotemporal modeling of mature‐at‐length data using a sliding window approach," Environmetrics, John Wiley & Sons, Ltd., vol. 34(2), March.
    17. François Bachoc & Marc G Genton & Klaus Nordhausen & Anne Ruiz-Gazen & Joni Virta, 2020. "Spatial blind source separation," Biometrika, Biometrika Trust, vol. 107(3), pages 627-646.
    18. Zhengyi Zhou & David S. Matteson & Dawn B. Woodard & Shane G. Henderson & Athanasios C. Micheas, 2015. "A Spatio-Temporal Point Process Model for Ambulance Demand," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(509), pages 6-15, March.
    19. Bondo, Kristin J. & Rosenberry, Christopher S. & Stainbrook, David & Walter, W. David, 2024. "Comparing risk of chronic wasting disease occurrence using Bayesian hierarchical spatial models and different surveillance types," Ecological Modelling, Elsevier, vol. 493(C).
    20. Daniel Cervone & Alex D’Amour & Luke Bornn & Kirk Goldsberry, 2016. "A Multiresolution Stochastic Process Model for Predicting Basketball Possession Outcomes," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(514), pages 585-599, April.

    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:compst:v:33:y:2018:i:4:d:10.1007_s00180-018-0805-z. 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.