Abstract
Survival analysis has received a great deal of attention as a subfield of Bayesian nonparametrics over the last 50 years. In particular, the fitting of survival models that allow for sophisticated correlation structures has become common due to computational advances in the 1990s, in particular Markov chain Monte Carlo techniques. Very large, complex spatial datasets can now be analyzed accurately including the quantification of spatiotemporal trends and risk factors. This chapter reviews four nonparametric priors on baseline survival distributions in common use, followed by a catalogue of semiparametric and nonparametric models for survival data. Generalizations of these models allowing for spatial dependence are then discussed and broadly illustrated. Throughout, practical implementation through existing software is emphasized.
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References
Aalen, O. O. (1980). A model for nonparametric regression analysis of counting processes. In Mathematical Statistics and Probability Theory, volume 2, pages 1–25. Springer-Verlag.
Aalen, O. O. (1989). A linear regression model for the analysis of life times. Statistics in Medicine, 8(8), 907–925.
Alzola, C. and Harrell, F. (2006). An Introduction to S and the Hmisc and Design Libraries. Online manuscript available at http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RS/sintro.pdf.
Andersen, P. K. and Gill, R. D. (1982). Cox’s regression model for counting processes: A large sample study. The Annals of Statistics, 10(4), 1100–1120.
Banerjee, S. and Carlin, B. P. (2003). Semiparametric spatio-temporal frailty modeling. Environmetrics, 14(5), 523–535.
Banerjee, S. and Dey, D. K. (2005). Semiparametric proportional odds models for spatially correlated survival data. Lifetime Data Analysis, 11(2), 175–191.
Banerjee, S., Wall, M. M., and Carlin, B. P. (2003). Frailty modeling for spatially correlated survival data, with application to infant mortality in Minnesota. Biostatistics, 4(1), 123–142.
Banerjee, S., Gelfand, A. E., Finley, A. O., and Sang, H. (2008). Gaussian predictive process models for large spatial data sets. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 70(4), 825–848.
Banerjee, S., Carlin, B. P., and Gelfand, A. E. (2015). Hierarchical Modeling and Analysis for Spatial Data, Second Edition. Chapman and Hall/CRC Press.
Bárdossy, A. (2006). Copula-based geostatistical models for groundwater quality parameters. Water Resources Research, 42(11), 1–12.
Belitz, C., Brezger, A., Klein, N., Kneib, T., Lang, S., and Umlauf, N. (2015). BayesX - Software for Bayesian inference in structured additive regression models. Version 3.0. Available from http://www.bayesx.org.
Berger, J. O. and Guglielmi, A. (2001). Bayesian and conditional frequentist testing of a parametric model versus nonparametric alternatives. Journal of the American Statistical Association, 96(453), 174–184.
Buckley, J. and James, I. (1979). Linear regression with censored data. Biometrika, 66(3), 429–436.
Burridge, J. (1981). Empirical Bayes analysis of survival time data. Journal of the Royal Statistical Society. Series B (Methodological), 43(1), 65–75.
Cai, B. and Meyer, R. (2011). Bayesian semiparametric modeling of survival data based on mixtures of B-spline distributions. Computational Statistics & Data Analysis, 55(3), 1260–1272.
Cai, B., Lin, X., and Wang, L. (2011). Bayesian proportional hazards model for current status data with monotone splines. Computational Statistics & Data Analysis, 55(9), 2644–2651.
Carlin, B. P. and Hodges, J. S. (1999). Hierarchical proportional hazards regression models for highly stratified data. Biometrics, 55(4), 1162–1170.
Chang, I.-S., Hsiung, C. A., Wu, Y.-J., and Yang, C.-C. (2005). Bayesian survival analysis using Bernstein polynomials. Scandinavian Journal of Statistics, 32(3), 447–466.
Chen, Y., Hanson, T., and Zhang, J. (2014). Accelerated hazards model based on parametric families generalized with Bernstein polynomials. Biometrics, 70(1), 192–201.
Chen, Y. Q. and Jewell, N. P. (2001). On a general class of semiparametric hazards regression models. Biometrika, 88(3), 687–702.
Chen, Y. Q. and Wang, M.-C. (2000). Analysis of accelerated hazards models. Journal of the American Statistical Association, 95(450), 608–618.
Cheng, S. C., Wei, L. J., and Ying, Z. (1995). Analysis of transformation models with censored data. Biometrika, 82(4), 835–845.
Chernoukhov, A. (2013). Bayesian Spatial Additive Hazard Model. Electronic Theses and Dissertations. Paper 4965. http://scholar.uwindsor.ca/etd/4965
Christensen, R. and Johnson, W. (1988). Modeling accelerated failure time with a Dirichlet process. Biometrika, 75(4), 693–704.
Clayton, D. G. (1991). A Monte Carlo method for Bayesian inference in frailty models. Biometrics, 47(2), 467–485.
Cox, D. R. (1972). Regression models and life-tables (with discussion). Journal of the Royal Statistical Society. Series B (Methodological), 34(2), 187–220.
Cox, D. R. (1975). Partial likelihood. Biometrika, 62(2), 269–276.
Dabrowska, D. M. and Doksum, K. A. (1988). Estimation and testing in a two-sample generalized odds-rate model. Journal of the American Statistical Association, 83(403), 744–749.
Darmofal, D. (2009). Bayesian spatial survival models for political event processes. American Journal of Political Science, 53(1), 241–257.
Dasgupta, P., Cramb, S. M., Aitken, J. F., Turrell, G., and Baade, P. D. (2014). Comparing multilevel and Bayesian spatial random effects survival models to assess geographical inequalities in colorectal cancer survival: a case study. International Journal of Health Geographics, 13(1), 36.
de Boor, C. (2001). A Practical Guide to Splines. Applied Mathematical Sciences, Vol. 27. Springer-Verlag: New York.
De Iorio, M., Johnson, W. O., Müller, P., and Rosner, G. L. (2009). Bayesian nonparametric nonproportional hazards survival modeling. Biometrics, 65(3), 762–771.
Devarajan, K. and Ebrahimi, N. (2011). A semi-parametric generalization of the Cox proportional hazards regression model: Inference and applications. Computational Statistics & Data Analysis, 55(1), 667–676.
Diva, U., Dey, D. K., and Banerjee, S. (2008). Parametric models for spatially correlated survival data for individuals with multiple cancers. Statistics in Medicine, 27(12), 2127–2144.
Dukić, V. and Dignam, J. (2007). Bayesian hierarchical multiresolution hazard model for the study of time-dependent failure patterns in early stage breast cancer. Bayesian Analysis, 2, 591–610.
Dunson, D. B. and Herring, A. H. (2005). Bayesian model selection and averaging in additive and proportional hazards. Lifetime Data Analysis, 11, 213–232.
Eilers, P. H. C. and Marx, B. D. (1996). Flexible smoothing with B-splines and penalties. Statistical Science, 11(2), 89–102.
Escobar, M. D. and West, M. (1995). Bayesian density estimation and inference using mixtures. Journal of the American Statistical Association, 90, 577–588.
Fahrmeir, L. and Kneib, T. (2011). Bayesian Smoothing and Regression for Longitudinal, Spatial and Event History Data. Oxford University Press.
Ferguson, T. S. (1973). A Bayesian analysis of some nonparametric problems. The Annals of Statistics, 1, 209–230.
Ferguson, T. S. (1974). Prior distributions on spaces of probability measures. The Annals of Statistics, 2, 615–629.
Finley, A. O., Sang, H., Banerjee, S., and Gelfand, A. E. (2009). Improving the performance of predictive process modeling for large datasets. Computational statistics & data analysis, 53(8), 2873–2884.
Furrer, R., Genton, M. G., and Nychka, D. (2006). Covariance tapering for interpolation of large spatial datasets. Journal of Computational and Graphical Statistics, 15(3), 502–523.
Geisser, S. and Eddy, W. F. (1979). A predictive approach to model selection. Journal of the American Statistical Association, 74, 153–160.
Gelfand, A. E. and Mallick, B. K. (1995). Bayesian analysis of proportional hazards models built from monotone functions. Biometrics, 51, 843–852.
Gray, R. J. (1992). Flexible methods for analyzing survival data using splines, with applications to breast cancer prognosis. Journal of the American Statistical Association, 87, 942–951.
Griffin, J. (2010). Default priors for density estimation with mixture models. Bayesian Analysis, 5, 45–64.
Hanson, T., Kottas, A., and Branscum, A. (2008). Modelling stochastic order in the analysis of receiver operating characteristic data: Bayesian nonparametric approaches. Journal of the Royal Statistical Society: Series C, 57, 207–225.
Hanson, T., Johnson, W., and Laud, P. (2009). Semiparametric inference for survival models with step process covariates. Canadian Journal of Statistics, 37(1), 60–79.
Hanson, T. E. (2006a). Inference for mixtures of finite Polya tree models. Journal of the American Statistical Association, 101(476), 1548–1565.
Hanson, T. E. (2006b). Modeling censored lifetime data using a mixture of gammas baseline. Bayesian Analysis, 1, 575–594.
Hanson, T. E. and Johnson, W. O. (2002). Modeling regression error with a mixture of Polya trees. Journal of the American Statistical Association, 97(460), 1020–1033.
Hanson, T. E. and Yang, M. (2007). Bayesian semiparametric proportional odds models. Biometrics, 63(1), 88–95.
Hanson, T. E., Branscum, A., and Johnson, W. O. (2005). Bayesian nonparametric modeling and data analysis: An introduction. In D. Dey and C. Rao, editors, Bayesian Thinking: Modeling and Computation (Handbook of Statistics, volume 25), pages 245–278. Elsevier: Amsterdam.
Hanson, T. E., Branscum, A., and Johnson, W. O. (2011). Predictive comparison of joint longitudinal–survival modeling: a case study illustrating competing approaches. Lifetime Data Analysis, 17, 3–28.
Hanson, T. E., Jara, A., Zhao, L., et al. (2012). A Bayesian semiparametric temporally-stratified proportional hazards model with spatial frailties. Bayesian Analysis, 7(1), 147–188.
Henderson, R., Shimakura, S., and Gorst, D. (2002). Modeling spatial variation in leukemia survival data. Journal of the American Statistical Association, 97(460), 965–972.
Hennerfeind, A., Brezger, A., and Fahrmeir, L. (2006). Geoadditive survival models. Journal of the American Statistical Association, 101(475), 1065–1075.
Hjort, N. L. (1990). Nonparametric Bayes estimators based on beta processes in models for life history data. The Annals of Statistics, 18, 1259–1294.
Hutton, J. L. and Monaghan, P. F. (2002). Choice of parametric accelerated life and proportional hazards models for survival data: Asymptotic results. Lifetime Data Analysis, 8, 375–393.
Ibrahim, J. G., Chen, M. H., and Sinha, D. (2001). Bayesian Survival Analysis. Springer-Verlag.
Jara, A. and Hanson, T. E. (2011). A class of mixtures of dependent tailfree processes. Biometrika, 98, 553–566.
Jara, A., Lesaffre, E., De Iorio, M., and Quitana, F. (2010). Bayesian semiparametric inference for multivariate doubly-interval-censored data. The Annals of Applied Statistics, 4(4), 2126–2149.
Jara, A., Hanson, T. E., Quintana, F. A., Müller, P., and Rosner, G. L. (2011). DPpackage: Bayesian semi- and nonparametric modeling in R. Journal of Statistical Software, 40(5), 1–30.
Johnson, W. O. and Christensen, R. (1989). Nonparametric Bayesian analysis of the accelerated failure time model. Statistics and Probability Letters, 8, 179–184.
Kalbfleisch, J. D. (1978). Nonparametric Bayesian analysis of survival time data. Journal of the Royal Statistical Society. Series B (Methodological), 40, 214–221.
Kaufman, C. G., Schervish, M. J., and Nychka, D. W. (2008). Covariance tapering for likelihood-based estimation in large spatial data sets. Journal of the American Statistical Association, 103(484), 1545–1555.
Kay, R. and Kinnersley, N. (2002). On the use of the accelerated failure time model as an alternative to the proportional hazards model in the treatment of time to event data: A case study in influenza. Drug Information Journal, 36, 571–579.
Kneib, T. (2006). Mixed model based inference in structured additive regression. Ludwig-Maximilians-Universität München.
Kneib, T. and Fahrmeir, L. (2007). A mixed model approach for geoadditive hazard regression. Scandinavian Journal of Statistics, 34(1), 207–228.
Koenker, R. (2008). Censored quantile regression redux. Journal of Statistical Software, 27(6), 1–25.
Koenker, R. and Hallock, K. F. (2001). Quantile regression. Journal of Economic Perspectives, 15, 143–156.
Komárek, A. and Lesaffre, E. (2007). Bayesian accelerated failure time model for correlated censored data with a normal mixture as an error distribution. Statistica Sinica, 17, 549–569.
Komárek, A. and Lesaffre, E. (2008). Bayesian accelerated failure time model with multivariate doubly-interval-censored data and flexible distributional assumptions. Journal of the American Statistical Association, 103, 523–533.
Kottas, A. and Gelfand, A. E. (2001). Bayesian semiparametric median regression modeling. Journal of the American Statistical Association, 95, 1458–1468.
Kuo, L. and Mallick, B. (1997). Bayesian semiparametric inference for the accelerated failure-time model. Canadian Journal of Statistics, 25, 457–472.
Lang, S. and Brezger, A. (2004). Bayesian P-splines. Journal of Computational and Graphical Statistics, 13, 183–212.
Lavine, M. (1992). Some aspects of Polya tree distributions for statistical modelling. The Annals of Statistics, 20, 1222–1235.
Lavine, M. (1994). More aspects of Polya tree distributions for statistical modelling. The Annals of Statistics, 22, 1161–1176.
Li, J. (2010). Application of copulas as a new geostatistical tool. Dissertation.
Li, J., Hong, Y., Thapa, R., and Burkhart, H. E. (2015a). Survival analysis of loblolly pine trees with spatially correlated random effects. Journal of the American Statistical Association, in press.
Li, L., Hanson, T., and Zhang, J. (2015b). Spatial extended hazard model with application to prostate cancer survival. Biometrics, in press.
Li, Y. and Lin, X. (2006). Semiparametric normal transformation models for spatially correlated survival data. Journal of the American Statistical Association, 101(474), 591–603.
Li, Y. and Ryan, L. (2002). Modeling spatial survival data using semiparametric frailty models. Biometrics, 58(2), 287–297.
Lin, X. and Wang, L. (2011). Bayesian proportional odds models for analyzing current status data: univariate, clustered, and multivariate. Communications in Statistics-Simulation and Computation, 40(8), 1171–1181.
Lin, X., Cai, B., Wang, L., and Zhang, Z. (2015). A Bayesian proportional hazards model for general interval-censored data. Lifetime Data Analysis, in press.
Liu, Y. (2012). Bayesian analysis of spatial and survival models with applications of computation techniques. Ph.D. thesis, University of Missouri–Columbia.
Lo, A. Y. (1984). On a class of Bayesian nonparametric estimates: I. Density estimates. Annals of Statistics, 12, 351–357.
Martinussen, T. and Scheike, T. H. (2006). Dynamic Regression Models for Survival Data. Springer-Verlag.
McKinley, T. J. (2007). Spatial survival analysis of infectious animal diseases. Ph.D. thesis, University of Exeter.
Müller, P. and Quintana, F. A. (2004). Nonparametric Bayesian data analysis. Statistical Science, 19(1), 95–110.
Müller, P., Quintana, F., Jara, A., and Hanson, T. (2015). Bayesian Nonparametric Data Analysis. Springer-Verlag: New York.
Murphy, S. A., Rossini, A. J., and van der Vaart, A. W. (1997). Maximum likelihood estimation in the proportional odds model. Journal of the American Statistical Association, 92, 968–976.
Neal, R. M. (2000). Markov chain sampling methods for Dirichlet process mixture models. Journal of Computational and Graphical Statistics, 9, 249–265.
Nelsen, R. B. (2006). An Introduction to Copulas. Springer, 2nd edition.
Nieto-Barajas, L. E. (2013). Lévy-driven processes in Bayesian nonparametric inference. Boletín de la Sociedad Matemática Mexicana, 19, 267–279.
Ojiambo, P. and Kang, E. (2013). Modeling spatial frailties in survival analysis of cucurbit downy mildew epidemics. Phytopathology, 103(3), 216–227.
Orbe, J., Ferreira, E., and Núñez Antón, V. (2002). Comparing proportional hazards and accelerated failure time models for survival analysis. Statistics in Medicine, 21(22), 3493–3510.
Pan, C., Cai, B., Wang, L., and Lin, X. (2014). Bayesian semi-parametric model for spatial interval-censored survival data. Computational Statistics & Data Analysis, 74, 198–209.
Petrone, S. (1999a). Bayesian density estimation using Bernstein polynomials. The Canadian Journal of Statistics, 27, 105–126.
Petrone, S. (1999b). Random Bernstein polynomials. Scandinavian Journal of Statistics, 26, 373–393.
Reid, N. (1994). A conversation with Sir David Cox. Statistical Science, 9, 439–455.
Ryan, T. and Woodall, W. (2005). The most-cited statistical papers. Journal of Applied Statistics, 32(5), 461–474.
Sang, H. and Huang, J. Z. (2012). A full scale approximation of covariance functions for large spatial data sets. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 74(1), 111–132.
Scharfstein, D. O., Tsiatis, A. A., and Gilbert, P. B. (1998). Efficient estimation in the generalized odds-rate class of regression models for right-censored time-to-event data. Lifetime Data Analysis, 4, 355–391.
Sethuraman, J. (1994). A constructive definition of Dirichlet priors. Statistica Sinica, 4, 639–650.
Sharef, E., Strawderman, R. L., Ruppert, D., Cowen, M., and Halasyamani, L. (2010). Bayesian adaptive B-spline estimation in proportional hazards frailty models. Electronic Journal of Statistics, 4, 606–642.
Sinha, D. and Dey, D. K. (1997). Semiparametric Bayesian analysis of survival data. Journal of the American Statistical Association, 92, 1195–1212.
Sinha, D., McHenry, M. B., Lipsitz, S. R., and Ghosh, M. (2009). Empirical Bayes estimation for additive hazards regression models. Biometrika, 96(3), 545–558.
Smith, M. S. (2013). Bayesian approaches to copula modelling. Bayesian Theory and Applications, pages 336–358.
Susarla, V. and Van Ryzin, J. (1976). Nonparametric Bayesian estimation of survival curves from incomplete observations. Journal of the American Statistical Association, 71, 897–902.
Therneau, T. M. and Grambsch, P. M. (2000). Modeling Survival Data: Extending the Cox Model. Springer-Verlag Inc.
Umlauf, N., Adler, D., Kneib, T., Lang, S., and Zeileis, A. (2015). Structured additive regression models: An R interface to BayesX. Journal of Statistical Software, 63(21), 1–46.
Walker, S. G. and Mallick, B. K. (1997). Hierarchical generalized linear models and frailty models with Bayesian nonparametric mixing. Journal of the Royal Statistical Society, Series B: Methodological, 59, 845–860.
Walker, S. G. and Mallick, B. K. (1999). A Bayesian semiparametric accelerated failure time model. Biometrics, 55(2), 477–483.
Wang, L. and Dunson, D. B. (2011). Semiparametric Bayes’ proportional odds models for current status data with underreporting. Biometrics, 67(3), 1111–1118.
Wang, S., Zhang, J., and Lawson, A. B. (2012). A Bayesian normal mixture accelerated failure time spatial model and its application to prostate cancer. Statistical Methods in Medical Research.
Yang, S. (1999). Censored median regression using weighted empirical survival and hazard functions. Journal of the American Statistical Association, 94, 137–145.
Yang, S. and Prentice, R. L. (1999). Semiparametric inference in the proportional odds regression model. Journal of the American Statistical Association, 94, 125–136.
Yin, G. and Ibrahim, J. G. (2005). A class of Bayesian shared gamma frailty models with multivariate failure time data. Biometrics, 61, 208–216.
Ying, Z., Jung, S. H., and Wei, L. J. (1995). Survival analysis with median regression models. Journal of the American Statistical Association, 90, 178–184.
Zellner, A. (1983). Applications of Bayesian analysis in econometrics. The Statistician, 32, 23–34.
Zhang, J. and Lawson, A. B. (2011). Bayesian parametric accelerated failure time spatial model and its application to prostate cancer. Journal of Applied Statistics, 38(3), 591–603.
Zhang, J., Peng, Y., and Zhao, O. (2011). A new semiparametric estimation method for accelerated hazard model. Biometrics, 67, 1352–1360.
Zhang, M. and Davidian, M. (2008). “Smooth” semiparametric regression analysis for arbitrarily censored time-to-event data. Biometrics, 64(2), 567–576.
Zhao, L. and Hanson, T. E. (2011). Spatially dependent Polya tree modeling for survival data. Biometrics, 67(2), 391–403.
Zhao, L., Hanson, T. E., and Carlin, B. P. (2009). Mixtures of Polya trees for flexible spatial frailty survival modelling. Biometrika, 96(2), 263–276.
Zhou, H., Hanson, T., and Zhang, J. (2015a). Generalized accelerated failure time spatial frailty model for arbitrarily censored data. Lifetime Data Analysis, in revision.
Zhou, H., Hanson, T., and Knapp, R. (2015b). Marginal Bayesian nonparametric model for time to disease arrival of threatened amphibian populations. Biometrics, in press.
Zhou, H., Hanson, T., Jara, A., and Zhang, J. (2015c). Modeling county level breast cancer survival data using a covariate-adjusted frailty proportional hazards model. The Annals of Applied Statistics, 9(1): 43–68.
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This work was supported by federal grants 1R03CA165110 and 1R03CA176739-01A1.
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Zhou, H., Hanson, T. (2015). Bayesian Spatial Survival Models. In: Mitra, R., Müller, P. (eds) Nonparametric Bayesian Inference in Biostatistics. Frontiers in Probability and the Statistical Sciences. Springer, Cham. https://doi.org/10.1007/978-3-319-19518-6_11
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