spBayesSurv: Fitting Bayesian Spatial Survival Models Using R

Abstract

Spatial survival analysis has received a great deal of attention over the last 20 years due to the important role that geographical information can play in predicting survival. This paper provides an introduction to a set of programs for implementing some Bayesian spatial survival models in R using the package spBayesSurv. The function survregbayes includes the three most commonly-used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. All manner of censored survival times are simultaneously accommodated including uncensored, interval censored, current-status, left and right censored, and mixtures of these. Left-truncated data are also accommodated. Time-dependent covariates are allowed under the piecewise constant assumption. Both georeferenced and areally observed spatial locations are handled via frailties. Model fit is assessed with conditional Cox-Snell residual plots, and model choice is carried out via the log pseudo marginal likelihood, the deviance information criterion and the WatanabeAkaike information criterion. The accelerated failure time frailty model with a covariatedependent baseline is included in the function frailtyGAFT. In addition, the package also provides two marginal survival models: proportional hazards and linear dependent Dirichlet process mixtures, where the spatial dependence is modeled via spatial copulas. Note that the package can also handle non-spatial data using non-spatial versions of the aforementioned models.