Skip to main content

Advertisement

Log in

Computationally tractable approximate and smoothed Polya trees

  • Published:
Statistics and Computing Aims and scope Submit manuscript

An Erratum to this article was published on 18 October 2016

This article has been updated

Abstract

A discrete approximation to the Polya tree prior suitable for latent data is proposed that enjoys surprisingly simple and efficient conjugate updating. This approximation is illustrated in two applied contexts: the implementation of a nonparametric meta-analysis involving studies on the relationship between alcohol consumption and breast cancer, and random intercept Poisson regression for Ache armadillo hunting treks. The discrete approximation is then smoothed with Gaussian kernels to provide a smooth density for use with continuous data; the smoothed approximation is illustrated on a classic dataset on galaxy velocities and on recent data involving breast cancer survival in Louisiana.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Change history

  • 18 October 2016

    An erratum to this article has been published.

References

  • Agresti, A.: Categorical Data Analysis. Wiley, New York (2002)

    Book  MATH  Google Scholar 

  • Aitchison, J., Shen, S.M.: Logistic-normal distributions: some properties and uses. Biometrika 67, 261–272 (1980)

    Article  MathSciNet  MATH  Google Scholar 

  • Aitkin, M.: A general maximum likelihood analysis of variance components in generalized linear models. Biometrics 55, 117–128 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  • Branscum, A., Hanson, T.: Bayesian nonparametric meta-analysis using Polya tree mixture models. Biometrics 64, 825–833 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  • Buckley, J.J., James, I.R.: Linear regression with censored data. Biometrika 66, 429–436 (1979)

    Article  MATH  Google Scholar 

  • Burr, D., Doss, H.: A Bayesian semiparametric model for random-effects meta-analysis. J. Am. Stat. Assoc. 100, 242–251 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  • Canale, A., Dunson, D.: Bayesian kernel mixtures for counts. J. Am. Stat. Assoc. 106, 1528–1539 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  • Canale, A., Dunson, D.B.: Multiscale Bernstein polynomials for densities. Stat. Sin. (in press, 2016)

  • Chen, Y., Hanson, T., Zhang, J.: Accelerated hazards model based on parametric families generalized with Bernstein polynomials. Biometrics 70, 192–201 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  • Christensen, R., Johnson, W., Branscum, A., Hanson, T.: Bayesian Ideas and Data Analysis: An Introduction for Scientists and Statisticians. CRC Press, Boca Raton (2010)

    MATH  Google Scholar 

  • Dempster, A.P., Laird, N.M., Rubin, D.B.: Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. B 39, 1–38 (1977)

    MathSciNet  MATH  Google Scholar 

  • Draper, D.: Discussion of Bayesian nonparametric inference for random distributions and related functions. J. R. Stat. Soc. B 61, 510–513 (1999)

    Google Scholar 

  • Escobar, M., West, M.: Bayesian density estimation and inference using mixtures. J. Am. Stat. Assoc. 90, 577–588 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  • Ferguson, T.S.: A Bayesian analysis of some nonparametric problems. Ann. Stat. 1, 209–230 (1973)

    Article  MathSciNet  MATH  Google Scholar 

  • Ferguson, T.S.: Prior distributions on spaces of probability measures. Ann. Stat. 02, 615–629 (1974)

    Article  MathSciNet  MATH  Google Scholar 

  • Follman, D.A., Lambert, D.: Generalizing logistic regression by nonparametric mixing. J. Am. Stat. Assoc. 84, 295–300 (1989)

    Article  Google Scholar 

  • Gamerman, D.: Sampling from the posterior distribution in generalized linear mixed models. Stat. Comput. 7, 57–68 (1997)

    Article  Google Scholar 

  • Gans, P., Gill, J.: Smoothing and differentiation of spectroscopic curves using spline functions. Appl. Spectrosc. 38, 370–376 (1984)

    Article  Google Scholar 

  • Geisser, S., Eddy, W.F.: A predictive approach to model selection. J. Am. Stat. Assoc. 74, 153–160 (1979)

    Article  MathSciNet  MATH  Google Scholar 

  • Gelfand, A.E., Dey, D.K.: Bayesian model choice: asymptotics and exact calculations. J. R. Stat. Soc. B 56, 501–514 (1994)

    MathSciNet  MATH  Google Scholar 

  • Ghidey, W., Lesaffre, E., Eilers, P.: Smooth random effects distribution in a linear mixed model. Biometrics 60, 945–953 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  • Ghosh, J.K., Ramamoorthi, R.V.: Bayesian Nonparametrics. Springer, New York (2003)

    MATH  Google Scholar 

  • Green, P.J.: Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82, 711–732 (1995)

    Article  MathSciNet  MATH  Google Scholar 

  • Hanson, T.: Inference for mixtures of finite Polya tree models. J. Am. Stat. Assoc. 101, 1548–1565 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  • Hanson, T., Jara, A.: Surviving fully Bayesian nonparametric regression models. In: Bayesian Theory and Applications, pp. 593–615. Oxford University Press, Oxford (2013)

  • Hanson, T., Johnson, W.: Modeling regression error with a mixture of Polya trees. J. Am. Stat. Assoc. 97, 1020–1033 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  • Harrell Jr., F.: rms: Regression Modeling Strategies. R Package Version 4.4-0 (2015)

  • Higdon, D.: Space and space–time modeling using process convolutions. In: Anderson, C., Barnett, V., Chatwin, P., El-Shaarawi, A. (eds.) Quantitative Methods for Current Environmental Issues, pp. 37–56. Springer, London (2002)

    Chapter  Google Scholar 

  • Hjort, N., Holmes, C., Müller, P., Walker, S.G. (eds.): Bayesian Nonparametrics. Cambridge Series in Statistical and Probabilistic Mathematics. Cambridge University Press, Cambridge (2010)

  • Ibrahim, J.G., Chen, M.H., Sinha, D.: Bayesian Survival Analysis. Springer, New York (2001)

    Book  MATH  Google Scholar 

  • Ishwaran, H., Zarepour, M.: Exact and approximate sum representations for the Dirichlet process. Can. J. Stat. 30, 269–283 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  • Jara, A., Hanson, T., Lesaffre, E.: Robustifying generalized linear mixed models using a new class of mixtures of multivariate Polya trees. J. Comput. Graph. Stat. 18, 838–860 (2009)

    Article  MathSciNet  Google Scholar 

  • Jara, A., Hanson, T., Quintana, F., Müeller, P., Rosner, G.: DPpackage: Bayesian semi- and nonparametric modeling in R. J. Stat. Softw. 40, 1–30 (2011). http://www.jstatsoft.org/v40/i05/

  • Kleinman, K.P., Ibrahim, J.G.: A semi-parametric Bayesian approach to generalized linear mixed models. Stat. Med. 17, 2579–2596 (1998)

    Article  Google Scholar 

  • Komárek, A., Lesaffre, E.: Generalized linear mixed model with a penalized Gaussian mixture as a random-effects distribution. Comput. Stat. Data Anal. 52, 3441–3458 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  • Komárek, A., Lesaffre, E., Hilton, J.: Accelerated failure time model for arbitrarily censored data with smoothed error distribution. J. Comput. Graph. Stat. 14, 726–745 (2005)

    Article  MathSciNet  Google Scholar 

  • Lavine, M.: Some aspects of Polya tree distributions for statistical modelling. Ann. Stat. 20, 1222–1235 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  • Lavine, M.: More aspects of Polya tree distributions for statistical modelling. Ann. Stat. 22, 1161–1176 (1994)

    Article  MATH  Google Scholar 

  • Longnecker, M.: Alcoholic beverage consumption in relation to risk of breast cancer: meta-analysis and review. Cancer Causes Control 5, 73–82 (1994)

    Article  Google Scholar 

  • Mauldin, R.D., Sudderth, W.D., Williams, S.C.: Polya trees and random distributions. Ann. Stat. 20, 1203–1221 (1992)

    Article  MATH  Google Scholar 

  • McMillan, G.: Ache residential grouping and social foraging. PhD Thesis, University of New Mexico (2001)

  • Mitra, R., Müller, P. (eds.): Nonparametric Bayesian Inference in Biostatistics. Frontiers in Probability and the Statistical Sciences. Springer, Cham (2015)

  • Müller, P., Quintana, F., Jara, A., Hanson, T.: Bayesian Nonparametric Data Analysis. Springer, Cham (2015)

    Book  MATH  Google Scholar 

  • R Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna (2014)

  • Roeder, K.: Density estimation with confidence sets exemplified by superclusters and voids in galaxies. J. Am. Stat. Assoc. 85, 617–624 (1990)

    Article  MATH  Google Scholar 

  • Sargent, D.J., Hodges, J.S., Carlin, B.P.: Structured Markov chain Monte Carlo. J. Comput. Graph. Stat. 9, 217–234 (2000)

    MathSciNet  Google Scholar 

  • Sethuraman, J.: A constructive definition of Dirichlet priors. Stat. Sin. 4, 639–650 (1994)

    MathSciNet  MATH  Google Scholar 

  • Unser, M., Aldroubi, A., Eden, M.: On the asymptotic convergence of B-spline wavelets to Gabor functions. IEEE Trans. Inf. Theory 38, 864–872 (1992)

    Article  MathSciNet  MATH  Google Scholar 

  • Wong, W.H., Ma, L.: Optional Polya tree and Bayesian inference. Ann. Stat. 38, 1433–1459 (2010)

    Article  MATH  Google Scholar 

  • Zhao, L., Hanson, T.: Spatially dependent Polya tree modeling for survival data. Biometrics 67, 391–403 (2011)

    Article  MathSciNet  MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to William Cipolli III.

Additional information

An erratum to this article is available at https://doi.org/10.1007/s11222-016-9686-6.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cipolli, W., Hanson, T. Computationally tractable approximate and smoothed Polya trees. Stat Comput 27, 39–51 (2017). https://doi.org/10.1007/s11222-016-9652-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11222-016-9652-3

Keywords

Navigation